Compositions comprising bacterial strains and use thereof in controlling pathogenic microorganisms

ABSTRACT

A composition comprising at least two bacterial strains selected from the group consisting of  Bacillus subtilis  281,  Bacillus subtilis  3,  Bacillus amyloliquefaciens  298 and a functional homolog of any of the preceding, wherein the composition does not comprise more than 5 different species of microbes, wherein:
         a sample of  Bacillus subtilis  281, has been deposited as KCTC 13468BP at the Korean Collection for Type Cultures;   a sample of  Bacillus subtilis  3, has been deposited as KCTC 13467BP at the Korean Collection for Type Cultures; and   a sample of  Bacillus amyloliquefaciens  298, has been deposited as KCTC 13469BP at the Korean Collection for Type Cultures. Also provided are methods that utilize the bacterial strains or functional homologs of same.

RELATED APPLICATIONS

This application is a US Continuation of PCT Patent Application No.PCT/IB2019/052016 having international filing date of Mar. 12, 2019which claims the benefit of priority under 35 USC § 119(e) of U.S.Provisional Patent Application Nos. 62/641,443, 62/641,444, 62/641,445and 62/641,464, all filed on Mar. 12, 2018. The contents of the aboveapplications are all incorporated by reference as if fully set forthherein in their entirety.

PCT Patent Application No. PCT/IB2019/052016 is also related to co-filedPCT Patent Application Nos. PCT/IB2019/052008, PCT/IB2019/052007,PCT/IB2019/052010, PCT/IB2019/052017 and PCT/IB2019/052014 entitled“CARTRIDGE FOR AN AUTOMATED AEROSOL DISPENSING DEVICE”, “ELECTRONICSAFETY FEATURE FOR AN AUTOMATED AEROSOL DISPENSING DEVICE”,“COMPOSITIONS COMPRISING BACTERIAL STRAINS AND USE THEREOF INCONTROLLING PATHOGENIC MICROORGANISMS”, “COMPOSITIONS COMPRISINGBACTERIAL STRAINS AND USE THEREOF IN CONTROLLING PATHOGENICMICROORGANISMS”, “COMPOSITIONS COMPRISING BACTERIAL STRAINS AND USETHEREOF IN CONTROLLING PATHOGENIC MICROORGANISMS” (Attorney Docket No.76907, 76908, 76909, 76910 and 76911). The contents of the aboveapplications are all incorporated by reference as if fully set forthherein in their entirety.

SEQUENCE LISTING STATEMENT

The ASCII file, entitled 84587SequenceListing.txt, created on Sep. 14,2020, comprising 15,755,105 bytes, submitted concurrently with thefiling of this application is incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates tocompositions comprising bacterial strains and use thereof in controllingpathogenic microorganisms.

A respiratory tract infection (RTI) refers to any of a number ofinfectious diseases involving the respiratory tract. An infection ofthis type is normally further classified as an upper respiratory tractinfection (URI or URTI) or a lower respiratory tract infection (LRI orLRTI). Lower respiratory infections, such as pneumonia, tend to be farmore serious conditions than upper respiratory infections, such as thecommon cold.

Identifying probiotic microbial strains which can be used in theeffective and safe treatment and prophylaxis of respiratory tractinfections is therefore highly desired.

Additional background art includes:

Jeon, Jung et al. 2016 J. Microbiol. Biotechnol 26(4): 666-674;

Cho 2008 Journal of Applied Biological Chemistry 51(6): 285-291;

U.S. Publication No. 20170348364;

U.S. Pat. No. 8,986,610.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present inventionthere is provided a composition comprising at least two bacterialstrains selected from the group consisting of Bacillus subtilis 281,Bacillus subtilis 3, Bacillus amyloliquefaciens 298 and a functionalhomolog of any of the preceding, wherein the composition does notcomprise more than 5 different species of microbes, wherein:

a sample of Bacillus subtilis 281, has been deposited as KCTC 13468BP atthe Korean Collection for Type Cultures;

a sample of Bacillus subtilis 3, has been deposited as KCTC 13467BP atthe Korean Collection for Type Cultures; and

a sample of Bacillus amyloliquefaciens 298, has been deposited as KCTC13469BP at the Korean Collection for Type Cultures.

According to an aspect of some embodiments of the present inventionthere is provided an article of manufacture comprising at least twobacterial strains selected from the group consisting of Bacillussubtilis 281, Bacillus subtilis 3, Bacillus amyloliquefaciens 298 and afunctional homolog of any of the preceding, wherein the composition doesnot comprise more than 5 different species of microbes, wherein:

a sample of Bacillus subtilis 281, has been deposited as KCTC 13468BP atthe Korean Collection for Type Cultures;

a sample of Bacillus subtilis 3, has been deposited as KCTC 13467BP atthe Korean Collection for Type Cultures; and

a sample of Bacillus amyloliquefaciens 298, has been deposited as KCTC13469BP at the Korean Collection for Type Cultures.

According to some embodiments of the invention, said bacterial strain orfunctional homolog of same is attached to a solid support.

According to some embodiments of the invention, said bacterial strain orfunctional homolog of same is soluble.

According to some embodiments of the invention, the article ofmanufacture comprises a commodity selected from the group consisting ofa food, a feed, a beverage, a pharmaceutical, a nutraceutical, acosmetic, a filter, a matrix and an aerosol system.

According to an aspect of some embodiments of the present inventionthere is provided an aerosol dispensing device comprising an effectiveamount of at least two bacterial strains selected from the groupconsisting of Bacillus subtilis 281, Bacillus subtilis 3, Bacillusamyloliquefaciens 298 and a functional homolog of any of the preceding,wherein the composition does not comprise more than 5 different speciesof microbes, wherein:

a sample of Bacillus subtilis 281, has been deposited as KCTC 13468BP atthe Korean Collection for Type Cultures;

a sample of Bacillus subtilis 3, has been deposited as KCTC 13467BP atthe Korean Collection for Type Cultures; and

a sample of Bacillus amyloliquefaciens 298, has been deposited as KCTC13469BP at the Korean Collection for Type Cultures.

According to some embodiments of the invention, the aerosol dispensingdevice is automated.

According to some embodiments of the invention, said bacterial strain orsaid functional homolog comprises a genomic nucleic acid sequence atleast 97% identical to the nucleic acid sequence set forth in SEQ ID NO:4, 6 or 8.

According to some embodiments of the invention, said bacterial strain orsaid functional homolog exhibits:

(i) growth inhibitory effects against bacteria and fungi, as shown inTables 3, 4, 8, 9, 13, 14, 18 and 19.

(ii) no lecithinase activity as determined by the absence of a whiteprecipitate when the isolated bacterial strain or functional homolog ofsame is streaked out onto egg yolk agar and incubated for 24 h at 37°C.; and

(iii) gamma hemolytic activity when streaked onto 5% sheep blood agarand incubated for 24 h at 37° C.

According to some embodiments of the invention, the bacterial strain orfunctional homolog of same is sensitive to an antibiotic selected fromthe group consisting of erythromycin, gentamicin, tetracycline,streptomycin, vancomycin, chloramphenicol, kanamycin and clindamycinaccording to the European Food Safety Authority MIC breakpoints forBacillus species.

According to some embodiments of the invention, the bacterial strain orfunctional homolog of same is incapable of colonizing a mammalian lung.

According to some embodiments of the invention, the bacterial strain orfunctional homolog of same exhibits growth inhibitory effects againstbacteria and fungi, as shown in Tables 3, 4, 8, 9, 13, 14, 18 and 19.

According to some embodiments of the invention, said functional homologis characterized by at least one of:

at least 70% DNA-DNA relatedness to the deposited strain with 5 uC orless DTm;

at least 97% genomic DNA sequence identity to the genomic DNA sequenceof the deposited strain;

having an average nucleotide identity (ANI) of at least about 97% withthe deposited strain;

having a tetranucleotide signature frequency correlation coefficient ofat least about 0.99 with the deposited strain;

having a Dice similarity coefficient;

being of the same ribotype as that of the deposited strain;

having a Pearson correlation coefficient of at least about 0.99 with thedeposited strain;

having a multilocus sequence typing (MLST) of at least about 0.99 withthe deposited strain;

having a functionality conserved gene that is at least about 97%identical to that of the deposited strain as determined at a level of asingle gene or multilocus sequence analysis (MLSA);

having a 16S nucleic acid sequence that is at least about 97% identicalto that of the deposited strain;

having substantially the same biochemical profiling as determined by theGEN III redox chemistry;

maintaining the coding and/or non-coding sequence order as that of thedeposited strain;

having the same codon usage as that of the deposited strain.

According to some embodiments of the invention, the composition, articleof manufacture or device comprises Bacillus subtilis 281, Bacillussubtilis 3 and Bacillus amyloliquefaciens 298 or a functional homolog ofsame.

According to some embodiments of the invention, said Bacillus subtilis281, Bacillus subtilis 3 and Bacillus amyloliquefaciens 298 or afunctional homolog of same are present in a ration of about 1:1:1.

According to an aspect of some embodiments of the present inventionthere is provided a method of controlling a population of pathogenicbacteria and/or fungi, the method comprising providing an effectiveamount of the composition, thereby controlling the population ofpathogenic bacteria and/or fungi.

According to some embodiments of the invention, said controlling isprophylactic.

According to some embodiments of the invention, said controlling istherapeutic.

According to some embodiments of the invention, said contactingcomprises in vivo contacting.

According to some embodiments of the invention, said contacting is byinhalation.

According to some embodiments of the invention, said contacting is byoral administration.

According to some embodiments of the invention, said contacting is byenteral administration.

According to some embodiments of the invention, said contacting is byparaenteral administration.

According to some embodiments of the invention, said contactingcomprises in vitro contacting.

According to some embodiments of the invention, said contacting is byusing the aerosol dispensing device.

Unless otherwise defined, all technical and/or scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which the invention pertains. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of embodiments of the invention, exemplarymethods and/or materials are described below. In case of conflict, thepatent specification, including definitions, will control. In addition,the materials, methods, and examples are illustrative only and are notintended to be necessarily limiting.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S)

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

Some embodiments of the invention are herein described, by way ofexample only, with reference to the accompanying drawings. With specificreference now to the drawings in detail, it is stressed that theparticulars shown are by way of example and for purposes of illustrativediscussion of embodiments of the invention. In this regard, thedescription taken with the drawings makes apparent to those skilled inthe art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 is a graph showing the survival rates of mice after respiratorytract infection (NC: negative control, BC: B. cereus, SP: S. pneumoniae,BS298: B. amyloliquefaciens 298).

FIG. 2 is a photograph showing the appearance of lungs in each groupdescribed in FIG. 1.

FIG. 3 is a photograph showing antagonism of pathogenic bacteria by B.amyloliquefaciens 298.

FIG. 4 is a photographic representation of results for the antagonism oftest molds using B. amyloliquefaciens 298 (A) and 10% hydrogen peroxide(B) as a positive control.

FIG. 5 is a graph showing Survival rates of mice after respiratory tractinfection (NC: negative control, BC: B. cereus, SP: S. pneumoniae, BS3:B. subtilis 3).

FIG. 6 is a photograph showing the appearance of lungs in each groupdescribed in FIG. 5.

FIG. 7 is a photograph showing antagonism of pathogenic bacteria by B.subtilis 3.

FIG. 8 is a photograph showing antagonism of molds using B. subtilis 3(A) and 10% hydrogen peroxide (B) as a positive control.

FIG. 9 is a graph showing the survival rates of mice after respiratorytract infection (NC: negative control, BC: B. cereus, SP: S. pneumoniae,BS281: B. subtilis 281).

FIG. 10 is a photograph showing the appearance of lungs in each groupdescribed in FIG. 9.

FIG. 11 is a photograph showing antagonism of pathogenic bacteria by B.subtilis 281.

FIG. 12 is a photographic representation of results for the antagonismof test molds using B. subtilis 281 (A) and 10% hydrogen peroxide (B) asa positive control.

FIG. 13 is a simplified schematic drawing of an example aerosoldispensing device in accordance with some example embodiments.

FIGS. 14A and 14B are simplified schematic drawings of an exampleaerosol dispensing device and an example replaceable cartridgerespectively in accordance with some example embodiments.

FIG. 15 is a simplified schematic drawing of an example replaceablecartridge installed in an example aerosol dispensing device inaccordance with some example embodiments.

FIG. 16 is simplified schematic drawing of an example aerosol dispensingdevice including one or more sensors in accordance with some exampleembodiments.

FIG. 17 is a graph showing the survival rates of mice after respiratorytract infection (NC: negative control, BC: B. cereus, SP: S. pneumoniae,BS3: B. subtilis 3, BS281: B. subtilis 281, BS298: B. amyloliquefaciens298).

FIG. 18 is a photograph showing the appearance of lungs in each groupdescribed in FIG. 17.

FIG. 19 is a photograph showing antagonism of pathogenic bacteria by B.subtilis 3, B. subtilis 281 and B. amyloliquefaiciens 298.

FIG. 20 is a photographic representation of results for the antagonismof test molds using B. subtilis strains 3 (A), B. subtilis 281 (B) andB. amyloliquefaciens 298 (C) and 10% hydrogen peroxide (D) as a positivecontrol.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates tocompositions comprising bacterial strains and use thereof in controllingpathogenic microorganisms. Before explaining at least one embodiment ofthe invention in detail, it is to be understood that the invention isnot necessarily limited in its application to the details set forth inthe following description or exemplified by the Examples. The inventionis capable of other embodiments or of being practiced or carried out invarious ways.

In a search for probiotic bacterial strains that can be effectively andsafely used in controlling pathogenic microorganisms, the presentinventors have identified a novel strains of Bacillus strains. Thepathogenicity of the strains was assessed using in-vitro methods such aslecithinase activity, hemolysis tests and resistance to therapeuticantibiotics. Safety was also evaluated in-vivo through a lung infectionmodel in mice. Lastly, the efficacy of the strains in inhibiting thegrowth of pathogenic microorganisms was affirmed in-vitro.

Collectively these assays place the compositions described according tosome embodiments as both safe for respiratory tract infection andfunctional with high potential to be used in various domestic, clinicaland industrial applications.

According to an aspect of some embodiments of the present inventionthere is provided a composition comprising at least two bacterialstrains selected from the group consisting of Bacillus subtilis 281,Bacillus subtilis 3, Bacillus amyloliquefaciens 298 and a functionalhomolog of any of the preceding, wherein the composition does notcomprise more than 5 different species of microbes, wherein:

a sample of Bacillus subtilis 281, has been deposited as KCTC 13468BP atthe Korean Collection for Type Cultures;

a sample of Bacillus subtilis 3, has been deposited as KCTC 13467BP atthe Korean Collection for Type Cultures; and

a sample of Bacillus amyloliquefaciens 298, has been deposited as KCTC13469BP at the Korean Collection for Type Cultures.

According to an aspect of some embodiments of the present inventionthere is provided an article of manufacture comprising at least twobacterial strains selected from the group consisting of Bacillussubtilis 281, Bacillus subtilis 3, Bacillus amyloliquefaciens 298 and afunctional homolog of any of the preceding, wherein the composition doesnot comprise more than 5 different species of microbes, wherein:

a sample of Bacillus subtilis 281, has been deposited as KCTC 13468BP atthe Korean Collection for Type Cultures;

a sample of Bacillus subtilis 3, has been deposited as KCTC 13467BP atthe Korean Collection for Type Cultures; and

a sample of Bacillus amyloliquefaciens 298, has been deposited as KCTC13469BP at the Korean Collection for Type Cultures.

According to some embodiments of the invention, said bacterial strain orfunctional homolog of same is attached to a solid support.

According to some embodiments of the invention, said bacterial strain orfunctional homolog of same is soluble.

According to some embodiments of the invention, the article ofmanufacture comprises a commodity selected from the group consisting ofa food, a feed, a beverage, a pharmaceutical, a nutraceutical, acosmetic, a filter, a matrix and an aerosol system.

According to an aspect of some embodiments of the present inventionthere is provided an aerosol dispensing device comprising an effectiveamount of at least two bacterial strains selected from the groupconsisting of Bacillus subtilis 281, Bacillus subtilis 3, Bacillusamyloliquefaciens 298 and a functional homolog of any of the preceding,wherein the composition does not comprise more than 5 different speciesof microbes, wherein:

a sample of Bacillus subtilis 281, has been deposited as KCTC 13468BP atthe Korean Collection for Type Cultures;

a sample of Bacillus subtilis 3, has been deposited as KCTC 13467BP atthe Korean Collection for Type Cultures; and

a sample of Bacillus amyloliquefaciens 298, has been deposited as KCTC13469BP at the Korean Collection for Type Cultures.

According to some embodiments of the invention, the aerosol dispensingdevice is automated.

According to some embodiments of the invention, said bacterial strain orsaid functional homolog comprises a genomic nucleic acid sequence atleast 97% identical to the nucleic acid sequence set forth in SEQ ID NO:4, 6 or 8.

According to some embodiments of the invention, said bacterial strain orsaid functional homolog exhibits:

(i) growth inhibitory effects against bacteria and fungi, as shown inTables 3, 4, 8, 9, 13, 14, 18 and 19.

(ii) no lecithinase activity as determined by the absence of a whiteprecipitate when the isolated bacterial strain or functional homolog ofsame is streaked out onto egg yolk agar and incubated for 24 h at 37°C.; and

(iii) gamma hemolytic activity when streaked onto 5% sheep blood agarand incubated for 24 h at 37° C.

According to some embodiments of the invention, the bacterial strain orfunctional homolog of same is sensitive to an antibiotic selected fromthe group consisting of erythromycin, gentamicin, tetracycline,streptomycin, vancomycin, chloramphenicol, kanamycin and clindamycinaccording to the European Food Safety Authority MIC breakpoints forBacillus species.

According to some embodiments of the invention, the bacterial strain orfunctional homolog of same is incapable of colonizing a mammalian lung.

According to some embodiments of the invention, the bacterial strain orfunctional homolog of same exhibits growth inhibitory effects againstbacteria and fungi, as shown in Tables 3, 4, 8, 9, 13, 14, 18 and 19.

According to some embodiments of the invention, said functional homologis characterized by at least one of:

at least 70% DNA-DNA relatedness to the deposited strain with 5 uC orless DTm;

at least 97% genomic DNA sequence identity to the genomic DNA sequenceof the deposited strain;

having an average nucleotide identity (ANI) of at least about 97% withthe deposited strain;

having a tetranucleotide signature frequency correlation coefficient ofat least about 0.99 with the deposited strain;

having a Dice similarity coefficient;

being of the same ribotype as that of the deposited strain;

having a Pearson correlation coefficient of at least about 0.99 with thedeposited strain;

having a multilocus sequence typing (MLST) of at least about 0.99 withthe deposited strain;

having a functionality conserved gene that is at least about 97%identical to that of the deposited strain as determined at a level of asingle gene or multilocus sequence analysis (MLSA);

having a 16S nucleic acid sequence that is at least about 97% identicalto that of the deposited strain;

having substantially the same biochemical profiling as determined by theGEN III redox chemistry;

maintaining the coding and/or non-coding sequence order as that of thedeposited strain;

having the same codon usage as that of the deposited strain.

According to some embodiments of the invention, the composition, articleof manufacture or device comprises Bacillus subtilis 281, Bacillussubtilis 3 and Bacillus amyloliquefaciens 298 or a functional homolog ofsame.

According to some embodiments of the invention, said Bacillus subtilis281, Bacillus subtilis 3 and Bacillus amyloliquefaciens 298 or afunctional homolog of same are present in a ration of about 1:1:1.

According to an aspect of some embodiments of the present inventionthere is provided a method of controlling a population of pathogenicbacteria and/or fungi, the method comprising providing an effectiveamount of the composition, thereby controlling the population ofpathogenic bacteria and/or fungi.

According to some embodiments of the invention, said controlling isprophylactic.

According to some embodiments of the invention, said controlling istherapeutic.

According to some embodiments of the invention, said contactingcomprises in vivo contacting.

According to some embodiments of the invention, said contacting is byinhalation.

According to some embodiments of the invention, said contacting is byoral administration.

According to some embodiments of the invention, said contacting is byenteral administration.

According to some embodiments of the invention, said contacting is byparaenteral administration.

According to some embodiments of the invention, said contactingcomprises in vitro contacting.

According to some embodiments of the invention, said contacting is byusing the aerosol dispensing device.

KCTC 13469BP has been deposited in the Korean Collection for TypeCultures, Korea Research Institute of Bioscience and Biotechnology(KRIBB) 181, Ipsin-gil, Jeongeup-si, Jeolllabuk-do 56212, Republic ofKorea on Jan. 25, 2018.

The bacterial strain can be as deposited or a variant thereof, alsoreferred to herein as a “functional homolog”.

KCTC 13467BP has been deposited in the Korean Collection for TypeCultures, Korea Research Institute of Bioscience and Biotechnology(KRIBB) 181, Ipsin-gil, Jeongeup-si, Jeolllabuk-do 56212, Republic ofKorea on Jan. 25, 2018.

The bacterial strain can be as deposited or a variant thereof, alsoreferred to herein as a “functional homolog”.

KCTC 13468BP has been deposited in the Korean Collection for TypeCultures, Korea Research Institute of Bioscience and Biotechnology(KRIBB) 181, Ipsin-gil, Jeongeup-si, Jeolllabuk-do 56212, Republic ofKorea on Jan. 25, 2018.

The bacterial strain can be as deposited or a variant thereof, alsoreferred to herein as a “functional homolog”.

The term “the microbial strain” or “the bacterial strain” can refer tothe deposited strain and/or the functional homolog.

As used herein “functional homolog” or “functionally homologous” or“variant” or a grammatical equivalent as used herein, refers to amodification (i.e., at least one mutation) of the deposited microbialstrain resulting in a microbial strain that is endowed withsubstantially the same ensemble of biological activities (+/−10%, 20%,40%, 50%, 60% when tested under the same conditions) as that of thedeposited strain (see hereinbelow and in the Examples section whichfollows) and can be classified to the same species or strain based onknown methods of species/strain classifications.

Following are non-limiting criteria for identifying a functionalhomolog. These criteria, which are mostly genetic, combined with thefunctional characteristic as defined hereinbelow and in the Examplessection, which follows, will be facilitate the skilled artisan indefining the scope of the functional homolog.

Thus, according to a specific embodiment, the deposited strain and thefunctional homolog belong to the same operational taxonomic units (OTU).

An “OTU” (or plural, “OTUs”) refers to a terminal leaf in a phylogenetictree and is defined by a nucleic acid sequence, e.g., the entire genome,or a specific genetic sequence, and all sequences that share sequenceidentity to this nucleic acid sequence at the level of species. In someembodiments the specific genetic sequence may be the 16S-rRNA sequenceor a portion of the 16S-rRNA (also referred to herein as “16S”) sequenceor other functionally conserved genes as listed below. In otherembodiments, the entire genomes of two entities are sequenced andcompared. In another embodiment, selected regions such as multilocussequence tags (MLST, MLSA), specific genes, or sets of genes may begenetically compared. In 16S-rRNA embodiments, OTUs that share at least97% average nucleotide identity across the entire 16S or some variableregion of the 16S are considered the same OTU (see e.g. Claesson M J,Wang Q, O'Sullivan O, Greene-Diniz R, Cole J R, Ros R P, and O'Toole PW. 2010. Comparison of two next-generation sequencing technologies forresolving highly complex microbiota composition using tandem variable16S rRNA gene regions. Nucleic Acids Res 38: e200. Konstantinidis K T,Ramette A, and Tiedje J M. 2006. The bacterial species definition in thegenomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940). Inembodiments involving the complete genome, MLSTs, specific genes, orsets of genes OTUs that share at least 95% average nucleotide identityare considered the same OTU (see e.g. Achtman M, and Wagner M. 2008.Microbial diversity and the genetic nature of microbial species. Nat.Rev. Microbiol. 6: 431-440. Konstantinidis K T, Ramette A, and Tiedje JM. 2006. The bacterial species definition in the genomic era. PhilosTrans R Soc Lond B Biol Sci 361: 1929-1940). OTUs are frequently definedby comparing sequences between organisms. Such characterization employs,e.g., WGS data or a whole genome sequence.

According to a specific embodiment, the classification is based onDNA-DNA pairing data and/or sequence identity to functionally conservedgenes or fragments thereof.

According to a specific embodiment a species/strain can be defined byDNA-DNA hybridization involving a pairwise comparison of two entiregenomes and reflects the overall sequence similarity between them.According to a specific embodiment, a species is defined as a set ofstrains with at least about 70%, e.g., at least about 75%, at leastabout 80%, at least about 85%, at least about 90%, at least about 91%,at least about 92%, at least about 93%, at least about 94%, at leastabout 95% or more DNA-DNA relatedness and with 5 uC or less DTm andhaving the activities as defined hereinbelow and in the Examples sectionwhich follows.

According to a specific embodiment, the genomic nucleic acid sequence isat least about 97%, at least about 97.1%, at least about 97.2%, at leastabout 97.3%, at least about 97.4%, at least about 97.5%, at least about97.6%, at least about 97.7%, at least about 97.8%, at least about 97.9%,at least about 98%, at least about 98.1%, at least about 98.2%, at leastabout 98.3%, at least about 98.4%, at least about 98.5%, at least about98.6%, at least about 98.7%, at least about 98.8%, at least about 98.9%,at least about 99%, at least about 99.1%, at least about 99.2%, at leastabout 99.3%, at least about 99.4%, at least about 99.5%, at least about99.6%, at least about 99.7%, at least about 99.8%, at least about 99.8%,at least about 99.9%, at least about 99.95% 99.95%, at least about99.99%, at least about 99.999%, at least about 99.9999%, at least about99.99999%, at least about 99.999999% or more DNA-DNA relatedness andwith 5 uC or less DTm and having the activities hereinbelow and in theExamples section which follows.

Thus, for example, if there is DNA-DNA hybridization on the basis of thearticle of Goris et al. [Goris, J., Konstantinidis, K. T., Klappenbach,J. A., Coenye, T., Vandamme, P., and Tiedje, J M. (2007). DNA-DNAhybridization values and their relationship to whole-genome sequencesimilarities. Int J Syst Evol Microbiol 57:81-91], some microorganismsexpressing a DNA-DNA relatedness value of 70% or more (as describedabove) can be regarded as functional homologs according to someembodiments of the invention.

According to a specific embodiment, the reference genomic sequence is asset forth in SEQ ID NO: 4, 6 or 8).

As used herein, “sequence identity” or “identity” or grammaticalequivalents as used herein in the context of two nucleic acid orpolypeptide sequences includes reference to the residues in the twosequences which are the same when aligned. When percentage of sequenceidentity is used in reference to proteins it is recognized that residuepositions which are not identical often differ by conservative aminoacid substitutions, where amino acid residues are substituted for otheramino acid residues with similar chemical properties (e.g. charge orhydrophobicity) and therefore do not change the functional properties ofthe molecule. Where sequences differ in conservative substitutions, thepercent sequence identity may be adjusted upwards to correct for theconservative nature of the substitution. Sequences which differ by suchconservative substitutions are considered to have “sequence similarity”or “similarity”. Means for making this adjustment are well-known tothose of skill in the art. Typically this involves scoring aconservative substitution as a partial rather than a full mismatch,thereby increasing the percentage sequence identity. Thus, for example,where an identical amino acid is given a score of 1 and anon-conservative substitution is given a score of zero, a conservativesubstitution is given a score between zero and 1. The scoring ofconservative substitutions is calculated, e.g., according to thealgorithm of Henikoff S and Henikoff J G. [Amino acid substitutionmatrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 1992,89(22): 10915-9].

Identity can be determined using any homology comparison software,including for example, the BlastN software of the National Center ofBiotechnology Information (NCBI) such as by using default parameters.

According to some embodiments of the invention, the identity is a globalidentity, i.e., an identity over the entire nucleic acid sequences ofthe invention and not over portions thereof.

According to a specific embodiment, the genomic nucleic acid sequence isat least about 70%, e.g., at least 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96% least about 97%, at least about 97.1%, at least about 97.2%,at least about 97.3%, at least about 97.4%, at least about 97.5%, atleast about 97.6%, at least about 97.7%, at least about 97.8%, at leastabout 97.9%, at least about 98%, at least about 98.1%, at least about98.2%, at least about 98.3%, at least about 98.4%, at least about 98.5%,at least about 98.6%, at least about 98.7%, at least about 98.8%, atleast about 98.9%, at least about 99%, at least about 99.1%, at leastabout 99.2%, at least about 99.3%, at least about 99.4%, at least about99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%,at least about 99.8%, at least about 99.9%, at least about 99.95%99.95%, at least about 99.99%, at least about 99.999%, at least about99.9999%, at least about 99.99999%, at least about 99.999999% or more tothe genomic sequence of the deposited strain (SEQ ID NO: 4, 6 or 8).

According to a specific embodiment, the genomic nucleic acid sequence isat least about 97%, at least about 97.1%, at least about 97.2%, at leastabout 97.3%, at least about 97.4%, at least about 97.5%, at least about97.6%, at least about 97.7%, at least about 97.8%, at least about 97.9%,at least about 98%, at least about 98.1%, at least about 98.2%, at leastabout 98.3%, at least about 98.4%, at least about 98.5%, at least about98.6%, at least about 98.7%, at least about 98.8%, at least about 98.9%,at least about 99%, at least about 99.1%, at least about 99.2%, at leastabout 99.3%, at least about 99.4%, at least about 99.5%, at least about99.6%, at least about 99.7%, at least about 99.8%, at least about 99.8%,at least about 99.9%, 99.95%, at least about 99.99%, at least about99.999%, at least about 99.9999%, at least about 99.99999%, at leastabout 99.999999% or more identical to that of the deposited strain (SEQID NO: 4, 6 or 8).

According to an additional or alternative embodiment, a functionalhomolog is determined as the average nucleotide identity (ANI), whichdetects the DNA conservation of the core genome (Konstantinidis K andTiedje J M, 2005, Proc. Natl. Acad. Sci. USA 102: 2567-2592). In someembodiments, the ANI between the functional homolog and the depositedstrain is of at least about 95%, at least about, 96%, at least about97%, at least about 98%, at least about 99%, at least about 99.1%, atleast about 99.5%, at least about 99.6%, at least about 99.7%, at leastabout 99.8%, at least about 99.9%, at least about 99.99%, at least about99.999%, at least about 99.9999%, at least about 99.99999%, at leastabout 99.999999% or more.

According to an additional or alternative embodiment, a functionalhomolog is determined by the degree of relatedness between thefunctional homolog and deposited strain determined as theTetranucleotide Signature Frequency Correlation Coefficient, which isbased on oligonucleotide frequencies (Bohlin J. et al. 2008, BMCGenomics, 9:104). In some embodiments, the Tetranucleotide SignatureFrequency Correlation coefficient between the variant and the depositedstrain is of about 0.99, 0.999, 0.9999, 0.99999, 0.999999, 0.999999 ormore.

According to an additional or alternative embodiment, the degree ofrelatedness between the functional homolog and the deposited strain isdetermined as the degree of similarity obtained when analyzing thegenomes of the parent and of the variant strain by Pulsed-field gelelectrophoresis (PFGE) using one or more restriction endonucleases. Thedegree of similarity obtained by PFGE can be measured by the Dicesimilarity coefficient. In some embodiments, the Dice similaritycoefficient between the variant and the deposited strain is of at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,at least about 99.1%, at least about 99.5%, at least about 99.6%, atleast about 99.7%, at least about 99.8%, at least about 99.9%, at leastabout 99.99%, at least about 99.999%, at least about 99.9999%, at leastabout 99.99999%, at least about 99.999999% or more.

According to an additional or alternative embodiment, the functionalhomolog is defined as having the same ribotype, as obtained using any ofthe methods known in the art and described, for instance, by Bouchet etal. (Clin. Microbiol. Rev., 2008, 21:262-273).

According to an additional or alternative embodiment, the degree ofrelatedness between the functional homolog and the deposited strain isdetermined by the Pearson correlation coefficient obtained by comparingthe genetic profiles of both strains obtained by repetitive extragenicpalindromic element-based PCR (REP-PCR) (see e.g. Chou and Wang, Int JFood Microbiol. 2006, 110:135-48). In some embodiments, the Pearsoncorrelation coefficient obtained by comparing the REP-PCR profiles ofthe variant and the deposited strain is of at least about 0.99, at leastabout 0.999, at least about 0.9999, at least about 0.99999, at leastabout 0.999999, at least about 0.999999 or more.

According to an additional or alternative embodiment, the degree ofrelatedness between the functional homolog and the deposited strains isdefined by the linkage distance obtained by comparing the geneticprofiles of both strains obtained by Multilocus sequence typing (MLST)(see e.g. Maiden, M. C., 1998, Proc. Natl. Acad. Sci. USA 95:3140-3145).In some embodiments, the linkage distance obtained by MLST of thefunctional homolog and the deposited strain is of at least about 0.99,at least about 0.999, at least about 0.9999, at least about 0.99999, atleast about 0.999999, at least about 0.999999 or more.

According to an additional or alternative embodiment, the functionalhomolog comprises a functionally conserved gene or a fragment thereofe.g., a house-keeping gene e.g., 16S-rRNA or Internal TranscribedSpacer” (ITS), recA, glnII, atpD, gap, glnA, gltA, gyrB, pnp, rpoB, thrCor dnaK that is at least about 97%, at least about 98%, at least about99%, at least about 99.1%, at least about 99.5%, at least about 99.6%,at least about 99.7%, at least about 99.8%, at least about 99.9%, atleast about 99.99%, at least about 99.999%, at least about 99.9999%, atleast about 99.99999%, at least about 99.999999% or more identical tothat of the deposited strain.

As mentioned, and according to a specific additional or an alternativeembodiment, a functional homolog can also be determined on the basis ofa multilocus sequence analysis (MLSA) determination of variousfunctionally conserved genes or fragments thereof e.g., at least one, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more functionallyconserved genes or fragments thereof, such as of e.g., 16S, ITS, recA,glnII, atpD, gap, glnA, gltA, gyrB, pnp, rpoB, thrC and dnaK.

According to a specific embodiment, the 16S ribosomal RNA (16S-rRNA)nucleic acid sequence is at least about 97%, e.g., at least about 97.1%,at least about 97.2%, at least about 97.3%, at least about 97.4%, atleast about 97.5%, at least about 97.6%, at least about 97.7%, at leastabout 97.8%, at least about 97.9%, at least about 98%, at least about98.1%, at least about 98.2%, at least about 98.3%, at least about 98.4%,at least about 98.5%, at least about 98.6%, at least about 98.7%, atleast about 98.8%, at least about 98.9%, at least about 99%, at leastabout 99.1%, at least about 99.2%, at least about 99.3%, at least about99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%,at least about 99.8%, at least about 99.8%, at least about 99.9%, atleast about 99.95%, at least about 99.999%, at least about 99.9999%, atleast about 99.99999%, at least about 99.999999% or more identical tothat of the deposited strain (SEQ ID NO: 3, 5 or 7).

According to a specific embodiment, the ITS nucleic acid sequence is atleast about 97%, e.g. at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the recA nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the atpD nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the dnaK nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the glnII nucleic acid sequence isat least about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the gap nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the glnA nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the gltA nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the gyrB nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the pnp nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the rpoB nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to a specific embodiment, the thrC nucleic acid sequence is atleast about 97%, e.g., at least about 97.1%, at least about 97.2%, atleast about 97.3%, at least about 97.4%, at least about 97.5%, at leastabout 97.6%, at least about 97.7%, at least about 97.8%, at least about97.9%, at least about 98%, at least about 98.1%, at least about 98.2%,at least about 98.3%, at least about 98.4%, at least about 98.5%, atleast about 98.6%, at least about 98.7%, at least about 98.8%, at leastabout 98.9%, at least about 99%, at least about 99.1%, at least about99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%,at least about 99.6%, at least about 99.7%, at least about 99.8%, atleast about 99.8%, at least about 99.9%, at least about 99.95%, at leastabout 99.999%, at least about 99.9999%, at least about 99.99999%, atleast about 99.999999% or more identical to that of the depositedstrain.

According to an additional or alternative embodiment the depositedstrain and the functional homolog is characterized by substantially thesame (+/−about 10%, 20%, 40%, 50%, 60% when tested under the sameconditions) biochemical profiling (e.g., biochemical fingerprinting)using for example, the GEN III redox chemistry (BIOLOG Inc. 21124 CabotBlvd. Hayward Calif., 94545, USA), which can analyze both Gram-negativeand Gram-positive bacteria, for their ability to metabolize all majorclasses of biochemicals, in addition to determining other importantphysiological properties such as pH, salt, and lactic acid tolerance.Further details can be obtained in “Modern Phenotypic MicrobialIdentification”, B. R. Bochner, Encyclopedia of Rapid MicrobiologicalMethods, 2006, v.2, Ch. 3, pp. 55-73, which is incorporated herein byreference in its entirety.

Example 7 of the Examples section provides a metabolite analysis of thedeposited strain.

According to an additional or alternative embodiment, the functionalhomolog is defined by a comparison of coding sequences (gene) order.

According to an additional or alternative embodiment, the functionalhomolog is defined by a comparison of order of non-coding sequences.

According to an additional or alternative embodiment, the functionalhomolog is defined by a comparison of order of coding and non-codingsequences.

According to some embodiments of the invention, the combined codingregion of the functional homolog is such that it maintains the originalorder of the coding regions as within the genomic sequence of thebacterial isolate yet without the non-coding regions.

Coding sequences of the deposited strain and their annotations areprovided in Table 5 of the Examples section which follows.

For example, in case the genomic sequence has the following codingregions, A, B, C, D, E, F, G, each flanked by non-coding sequences(e.g., regulatory elements, introns and the like), the combined codingregion will include a single nucleic acid sequence having theA+B+C+D+E+F+G coding regions combined together while maintaining theoriginal order of their genome, yet without the non-coding sequences.

According to some embodiments of the invention, the combined non-codingregion of the functional homolog is such that it maintains the originalorder of the non-coding regions as within the genomic sequence of thebacterial isolate yet without the coding regions as originally presentin the bacterial deposit.

According to some embodiments of the invention, the combined non-codingregion and coding region (i.e., the genome) of the functional homolog issuch that it maintains the original order of the coding and non-codingregions as within the genomic sequence of the microbial deposit.

As used herein “maintains” relate to at least about 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99% or 100% is maintained as compared to thedeposited strain.

According to an additional or alternative embodiment, the functionalhomolog is defined by a comparison of gene content.

According to a specific embodiment, the functional homolog comprises acombined coding region where at least about 90%, at least about 91%, atleast about 92%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, or more (e.g., 100%) is identical to a combined codingregion existing in genome of the deposited strain.

As used herein “combined coding region” refers to a nucleic acidsequence including all of the coding regions of the bacterial isolateyet without the non-coding regions of the bacterial isolate.

According to an additional or alternative embodiment, the functionalhomolog is defined by a comparison of nucleotide composition and codonusage.

According to an additional or alternative embodiment, the functionalhomolog is defined by a method based on random genome fragments and DNAmicroarray technology. These methods are of sufficiently high resolutionto for strain-to-species level identification.

One of ordinary skill in the art, based on knowledge of theclassification criteria would know how to identify strains that areconsidered functional homologs.

An additional and more detailed description of species-to-strainclassification can be found in:

Cho and Tiedje 2001 Bacterial species determination from DNA-DNAhybridization by using genome fragments and DNA microarrays;

Coenye et al. 2005 Towards a prokaryotic genomic taxonomy. FEMSMicrobiol. Rev. 29:147-167;

Konstantinidis and Tiedje (2005) Genomic insights that advance thespecies definition for prokaryotes. Proc. Natl. Acad. Sci. USA102:189-197;

Konstantinidis et al. 2006 Toward a more robust assessment ofintraspecies diversity using fewer genetic markers. Appl. Environ.Microbiol. 72:7286-7293.

It is to be understood that one or more methods as described herein canbe used to identify a functional homolog.

Genomic data can be obtained by methods which are well known in the arte.g., DNA sequencing, bioinformatics, electrophoresis, an enzyme-basedmismatch detection assay and a hybridization assay such as PCR, RT-PCR,RNase protection, in-situ hybridization, primer extension, Southernblot, Northern Blot and dot blot analysis.

According to a specific embodiment, the functional homolog and thedeposited strain belong to the same species (Bacillusamyloliquefaciens).

According to a specific embodiment, the functional homolog and thedeposited strain belong to the same sub-species.

As mentioned, the functional homolog is endowed with or maintains (asdefined herein) the functional properties of the deposited strain.

Thus according to a specific embodiment, the bacterial strain has nolecithinase activity as determined by the absence of a white precipitatewhen the isolated bacterial strain or functional homolog of same isstreaked out onto egg yolk agar and incubated for 24 h at 37° C.

According to an additional or an alternative embodiment, the bacterialstrain exhibits gamma hemolytic activity when streaked onto 5% sheepblood agar and incubated for 24 h at 37° C.

According to an additional or an alternative embodiment, the bacterialstrain is sensitive to an antibiotic selected from the group consistingof erythromycin, gentamicin, tetracycline, streptomycin, vancomycin,chloramphenicol, kanamycin and clindamycin according to the EuropeanFood Safety Authority MIC breakpoints for Bacillus species such as shownin Table 2 hereinbelow.

According to an additional or an alternative embodiment, the bacterialstrain is incapable of colonizing a mammalian (e.g., murine) lung.

According to an additional or an alternative embodiment, the bacterialstrain is growth inhibitory effects against bacteria and fungi, as shownin Tables 3 and 4, respectively.

-   -   According to an additional or an alternative embodiment, the        bacterial strain exhibits a secreted metabolome composition as        shown in the Examples section which follows. As used herein        “isolated” refers to an isolate of bacteria in which the        prevalence (i.e., concentration) of the bacterial stain or        functional homolog is enriched over that (exceeds that) found in        nature (e.g., in Doenjang, a fermented soybean paste). Thus, the        present teachings refer to cultures, preparations, compositions        (interchangeably used), which comprise the bacterial strain.

The isolated bacterial strain can be comprised in a composition,preparation, formulation, culture, article of manufacture.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture, comprises more than 1microbial strains or species.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture, comprises 2 microbialstrains or species.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture, comprises 3 microbialstrains or species.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture, comprises 4 microbialstrains or species.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture does not comprise more than5 different species or strains of microbes.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture does not comprise more than4 different species or strains of microbes.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture does not comprise more than3 different species or strains of microbes.

According to some embodiments, the composition, preparation,formulation, culture, article of manufacture does not comprise more than2 different species or strains of microbes.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises lessthan 10 microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises lessthan 9 microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises lessthan 8 microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises lessthan 7 microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises lessthan 6 microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises lessthan 5 microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises 4microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises 3microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises 2microbial species.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises 3microbial strains.

According to some embodiments of the invention, the composition,preparation, formulation, culture, article of manufacture comprises 2microbial strains.

According to a specific embodiment of the invention, the composition,preparation, formulation, culture, article of manufacture comprises asingle microbial species i.e., the isolated bacterial stain.

According to a specific embodiment, the composition, preparation,formulation, culture, article of manufacture comprises the bacterialstrain at a level of purity of at least about 20%, at least about 30%,at least about 40%, at least about 50%, at least about 60%, at leastabout 70%, at least about 80%, at least about 85%, at least about 90%,at least about 91%, at least about 92%, at least about 93%, at leastabout 94%, at least about 95%, 96%, at least about, 97%.

According to a specific embodiment, the composition, preparation,formulation, culture, article of manufacture comprises the bacterialstrain at a level of purity of at least about 98%, at least about 99%,at least about 99.1%, at least about 99.2%, at least about 99.3%, atleast about 99.4%, at least about 99.5%, at least about 99.6%, at leastabout 99.7%, at least about 99.8%, at least about 99.9%, at least about99.95%, at least about 99.99% or more, say 100% pure.

According to a specific embodiment, the microbial strain comprisesviable (more than 50%) microbial cells.

As used herein “viable” refers to a microorganism that is alive andcapable of regeneration and/or propagation, while in a vegetative,frozen, preserved, or reconstituted state.

According to a specific embodiment, the microbial strain comprisesspores of the bacterial strain.

As used herein ““spores” or “endospores” refer to microbes that aregenerally viable, more resistant to environmental influences such asheat and bactericidal than other forms of the same bacterial species,and typically capable of germination and out-growth. Bacteria that are“capable of forming spores” are those bacteria comprising the genes andother necessary abilities to produce spores under suitable environmentalconditions.

As used in herein, the term “CFUs” or “Colony Forming Units” refers tothe number of microbial cells e.g., bacterial strain, in a definedsample (e g milliliter of liquid, gram of powder) that form colonies andthereafter numbered, on a semi-solid bacteriological growth medium.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10²CFUs-10⁹ CFUs/gr powder or 10² CFUs-10⁹ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10²CFUs-10⁸ CFUs/gr powder or 10² CFUs-10⁸ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10²CFUs-10⁷ CFUs/gr powder or 10² CFUs-10⁷ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10²CFUs-10⁶ CFUs/gr powder or 10² CFUs-10⁶ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of According to a specificembodiment, the composition, preparation, formulation, culture, articleof manufacture comprises the bacterial strain at a level of purity of10² CFUs-10⁵ CFUs/gr powder or 10² CFUs-10⁵ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10²CFUs-10⁴ CFUs/gr powder or 10² CFUs-10⁴ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10²CFUs-10³ CFUs/gr powder or 10² CFUs-10³ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10³CFUs-10⁹ CFUs/gr powder or 10³ CFUs-10⁹ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10⁴CFUs-10⁹ CFUs/gr powder or 10⁴ CFUs-10⁹ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10⁵CFUs-10⁹ CFUs/gr powder or 10⁵ CFUs-10⁹ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10⁶CFUs-10⁹ CFUs/gr powder or 10⁶ CFUs-10⁹ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10⁷CFUs-10⁹ CFUs/gr powder or 10⁷ CFUs-10⁹ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10⁸CFUs-10⁹ CFUs/gr powder or 10⁸ CFUs-10⁹ CFUs/ml.

According to specific embodiments, the enrichment in the composition,preparation, formulation, culture, article of manufacture is 10⁸CFUs-10⁹ CFUs/gr powder or 10⁸ CFUs-10⁹ CFUs/ml.

According to a specific embodiment the composition, preparation,formulation, culture, article of manufacture comprises at least about100 CFUs or spores, at least about 10² CFUs/gr or CFUs/ml, at leastabout 10² CFUs/gr or CFUs/ml, at least about 10³ CFUs/gr or CFUs/ml, atleast about 10⁴ CFUs/gr or CFUs/ml, at least about 10⁵ CFUs/gr orCFUs/ml, at least about 10⁶ CFUs/gr or CFUs/ml, at least about 10⁷CFUs/gr or CFUs/ml, at least about 10⁸ CFUs/gr or CFUs/ml, at leastabout 10⁹ CFUs/gr or CFUs/ml, at least about 10¹⁰ CFUs/gr or CFUs/ml, atleast about 10¹¹ CFUs/gr or CFUs/ml, at least about 10¹² CFUs/gr orCFUs/ml.

According to a specific embodiment the composition, preparation,formulation, culture, article of manufacture (especially for a liquidformulation) comprises at least about 10⁶ CFUs/gr or CFUs/ml, at leastabout 10⁷ CFUs/gr or CFUs/ml, at least about 10⁸ CFUs/gr or CFUs/ml, atleast about 10⁹ CFUs/gr or CFUs/ml.

According to a specific embodiment the composition, preparation,formulation, culture, article of manufacture (especially for a dryformulation) comprises at least about 10⁸ CFUs/gr or CFUs/ml, at leastabout 10⁹ CFUs/gr or CFUs/ml, at least about 10¹⁰ CFUs/gr or CFUs/ml, atleast about 10¹¹ CFUs/gr or CFUs/ml, at least about 10¹² CFUs/gr orCFUs/ml.

According to a specific embodiment, the composition, preparation,formulation, culture, article of manufacture is selected from the groupconsisting of a still culture, whole cultures stored stock of cells(particularly glycerol stocks), agar strip, stored agar plug inglycerol/water, freeze dried stock, and dried stocks such aslyophilisate dried onto filter paper.

According to a specific embodiment, the composition, preparation,culture or formulation is devoid of animal contaminants to render itsafe for human use.

As used herein “a culture” refers to a fluid, pellet, scraping, driedsample, lyophilisate or a support, container, or medium such as a plate,paper, filter, matrix, straw, pipette or pipette tip, fiber, needle,gel, swab, tube, vial, particle, etc. that contains the deposited strainor the functional homolog thereof in an amount that exceeds that foundin nature, as described hereinabove. In the present invention, anisolated culture of a microbial strain is a culture fluid or a scraping,pellet, dried composition, preparation, formulation, culture, article ofmanufacture, lyophilisate, or a support, container, or medium thatcontains the microorganism, in the absence of other organisms (or incombination with other microbes which were preselected and grown for thepurpose of combined administration).

According to a specific embodiment, the bacterial strain within thecomposition, preparation, formulation, culture, article of manufactureis viable.

The bacterial strain can be produced or manufactured using methods whichare well known in the art of microbiology.

According to a specific embodiment, the microbial strain is isolatedfrom Doenjang, such as by using Luria Bertani Miller agar (BD, Difco)agar for plating. According to a specific embodiment, representativecolonies are picked from plates with the highest dilution still showingcolonies. After purification, the strain was stored at −80° C. The stockculture is propagated in LB Miller broth.

According to an aspect, the bacterial strain is cultured underconditions that allow propagation; after which (and/or during which) thebacterial strain is harvested.

Thus, according to some embodiments, cultures of the microbial strainmay be prepared using standard static drying and liquid fermentationtechniques known in the art. Growth is commonly effected in abioreactor.

A bioreactor refers to any device or system that supports a biologicallyactive environment. As described herein a bioreactor is a vessel inwhich microorganisms including the microorganism of the invention can begrown. A bioreactor may be any appropriate shape or size for growing themicroorganisms. A bioreactor may range in size and scale from 10 mL(e.g., small scale) to liter's to cubic meters (e.g., large scale) andmay be made of stainless steel, disposable material (e.g., nylon,plastic bags) or any other appropriate material as known and used in theart. The bioreactor may be a batch type bioreactor, a fed batch type ora continuous-type bioreactor (e.g., a continuous stirred reactor). Forexample, a bioreactor may be a chemostat as known and used in the art ofmicrobiology for growing and harvesting microorganisms. A bioreactor maybe obtained from any commercial supplier (See also Bioreactor SystemDesign, Asenjo & Merchuk, CRC Press, 1995).

For small scale operations, a batch bioreactor may be used, for example,to test and develop new processes, and for processes that cannot beconverted to continuous operations.

Microorganisms grown in a bioreactor may be suspended or immobilized.Growth in the bioreactor is generally under aerobic conditions atsuitable temperatures and pH for growth. For the organisms of theinvention, cell growth can be achieved at temperatures between 5-40° C.,with an exemplary temperature range selected from 20 to 10° C., 15 to28° C., 20 to 30° C., or 15 to 25° C. The pH of the nutrient medium canvary between 4.0 and 9.0. For example, the operating range can beusually slightly acidic to neutral at pH 5.0 to 8.5, or 4.5 to 6.5, orpH 5.0 to 6.0.

According to a specific embodiment, the cell growth is achieved at20-40° C. at pH of 5.0-8.5.

Typically, maximal cell yield is obtained in 20-72 hours afterinoculation. By virtue of the conditions applied in the selectionprocess and general requirements of most microorganisms, a person ofordinary skill in the art would be able to determine essential nutrientsand conditions. The microorganisms would typically be grown in aerobicliquid cultures on media which contain sources of carbon, nitrogen, andinorganic salts that can be assimilated by the microorganism andsupportive of efficient cell growth. Exemplary carbon sources arehexoses such as glucose, but other sources that are readily assimilatedsuch as amino acids, may be substituted. Many inorganic andproteinaceous materials may be used as nitrogen sources in the growthprocess. Exemplary nitrogen sources are amino acids and urea but othersinclude gaseous ammonia, inorganic salts of nitrate and ammonium,vitamins, purines, pyrimidines, yeast extract, beef extract, proteosepeptone, soybean meal, hydrolysates of casein, distiller's solubles, andthe like. Among the inorganic minerals that can be incorporated into thenutrient medium are the customary salts capable of yielding calcium,zinc, iron, manganese, magnesium, copper, cobalt, potassium, sodium,molybdate, phosphate, sulfate, chloride, borate, and like ions.

The culture can be a pure culture, whereby a single microbial strain isincluded or a mixed culture. This is of course pending the compliance ofthe microbial strains to co-exist and proliferate under the sameculturing conditions. When needed, an antibiotic or othergrowth-restricting conditions can be employed during culturing torestrict the growth of other microorganisms (contaminants) not desiredin the culture/co-culture e.g., temperature, essential nutrients and thelike.

According to an alternative or an additional embodiment, the desiredcombination is produced following culturing, such as when the microbialstrains do not share the same or optimal culturing conditions.

The ratio of each type of microorganism in the final product will dependon the intended use (some are listed hereinbelow).

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is10:1:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:1:10.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:10:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:10:10.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is10:10:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is10:1:10.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is5:1:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:1:5.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:5:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:5:5.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is5:5:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is5:1:5.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is2:1:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:1:2.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:2:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:2:2.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is2:2:1.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is2:1:2.

According to a specific embodiment the ration between the B.amyloliquefaciens 298, B. subtilis 3 and B. subtilis 281 strains is1:1:1.

The identity of the microorganism(s) in the culture can beexperimentally validated at the nucleic acid level, protein level,metabolite levels, functional level and/or by using classicalmicrobiology tools, e.g., streaking (e.g., with selection).

After production, the microbial strain can be stored or used fresh,either as is or subject to further formulation.

Also contemplated herein are a lysate and/or a fermentation product ofthe above described methods. Methods of cell lysis of bacterial strainse.g., of the species B. amyloliquefaciens are well known in the art.

The formulation of the microbial strain much depends on the intendeduse. Following is a non-limiting description of various formulationsthat can be used along with the present teachings.

According to a specific embodiment, the bacterial strain is formulatedin a liquid formulation.

According to a specific embodiment, the bacterial strain is formulatedin a dry formulation.

According to a specific embodiment, the bacterial strain is formulatedin a gel formulation.

Microbial strains formulations used to reduce the incidence ofpathogenic microorganisms (bacteria and/or fungi), can be in vivoadministered, can be released into the air or in conjunction with anHVAC system, applied to waste, food products, food processing areas,food preparation tools, agricultural products, agricultural water(irrigation water, agricultural soils, agricultural crops) and the like.The formulations of bacteria described herein can be applied in apowder, liquid, foam, gelled, aerosol or solid form. In liquidformulations, the microbial strain formulations may be dispensed fromconventional dispensing devices, including pump sprayers, aerosolcontainers, squirt bottles etc. For application over larger areas,hoses, sprinkler systems or other suitable devices may be used. In thealternative, the formulations can be applied as a dry powder such aslyophilized bacteria or using any of the techniques currently known to aperson of skill in the art. The optimal frequency of applications of themicrobial strain formulations may depend on the target on which theformulation is to be applied. In certain embodiments, whereinformulations are contemplated, a microorganism is harvested andconcentrated using a method that does not markedly decrease the viablecell concentration through centrifugation or filtration.

In embodiments wherein formulations are contemplated for preservation,such preservation may include a process of freezing, freeze-dryingand/or spray-drying.

In certain embodiments, the preserved cells can be used in amicrobial-based product. The preserved bacterial strain can be provided“as-is” without further dilution or modification. Additionally, incertain embodiments, the bacterial strain can be mixed with a carrier todilute the concentration of cells to an appropriate concentration foradministration. The carrier can be as simple as one element, or a morecomplex molecule or mixture of molecules in any proportion in order toact as a suitable carrier. This carrier and composition may, in certaininstances, have defined properties such as solubility in water or othermedia. The diluting carrier can be of any composition or combinationincluding but not limited to: lactose, glucose, non-fat dry milk powder,oligosaccharides, glycerol, oil, lecithin, or other materials.

In particular formulations, other chemicals or materials may be used toreduce or absorb moisture and/or oxygen for further protection andpreservation of the viable microbial cells. Such chemicals or materialsinclude, but are not limited to: calcium stearate, sodiumaluminosilicate, sodium sulfide, sodium carbonate, silica, iron oxides,calcium carbonate, zeolite, bicarbonates, sodium sulfate, silicondioxide and other silica materials.

In certain embodiments, a microbial strain formulation foradministration to a subject or a surface or other target can include apreservation matrix, which contains and preserves the culture. Such amatrix may include a biologically active binding agent, an antioxidant,a polyol, a carbohydrate and a proteinaceous material.

Antioxidants included in a preservation matrix may be provided to retardoxidative damage to the microbial cells during the preservation andstorage process.

Polyols (i.e., polyhydric alcohols) included in a preservation matrixmay be provided to maintain the native, uncollapsed state of cellularproteins and membranes during the preservation and storage process. Inparticular, polyols interact with the cell membrane and provide supportduring the dehydration portion of the preservation process. Examples ofpolyols include, but are not limited to xylitol, adonitol, glycerol,dulcitol, inositol, mannitol, sorbitol and/or arabitol.

Carbohydrates included in a preservation matrix may be provided tomaintain the native, uncollapsed state of cellular proteins andmembranes during the preservation and storage process. In particular,carbohydrates provide cell wall integrity during the dehydration portionof the preservation process. Exemplary carbohydrates include, but arenot limited to dextrose, lactose, maltose, sucrose, fructose and/or anyother monosaccharide, disaccharide or polysaccharide.

A proteinaceous material included in a preservation matrix may providefurther protection of the microbial cell during the dehydration portionof the preservation process. Exemplary proteinaceous materials include,but are not limited to skim milk and albumin.

The microbial cells can be preserved within a preservation matrixincluding coating the cell matrix suspension onto an inert carrier e.g.,a maltodextrin bead. The coated beads can then be dried, e.g., by afluid bed drying method. Fluid bed drying methods are well known in theart. The coated beads can be stored as a powder, placed into gelatincapsules, or pressed into tablets.

In other formulations, the microbial strain contemplated can beformulated as a hard gelatin capsule. Gelatin capsules are commerciallyavailable and are well known in the art. In this embodiment, the methodfurther comprises dispensing the cell suspension matrix to a gelatincapsule, chilling the gelatin capsule until the cell suspension matrixforms a non-fluid matrix and to affix the gel to the interior wall ofthe gelatin capsule, and desiccating the gelatin capsule in adesiccation chamber. Further examples of embodiments of preservationmatrices and gelatin capsule formulations may be found in U.S. Pat. No.6,468,526 which is herein incorporated by reference in its entirety.

In certain applications, the microbial strain may be placed in amicroencapsulation formulation. Such microencapsulation formulations mayhave applicability for example in administration to subjects via oral,nasal, rectal, vaginal or urethral routes. Spray drying is the mostcommonly used microencapsulation method in the food industry, iseconomical and flexible, and produces a good quality product. Theprocess involves the dispersion of the core material into a polymersolution, forming an emulsion or dispersion, followed by homogenisationof the liquid, then atomisation of the mixture into the drying chamber.This leads to evaporation of the solvent (water) and hence the formationof matrix type microcapsules.

Examples of microencapsulation can be found for example in U.S. Pat. No.5,641,209 that is herein incorporated by reference.

An embodiment of preserving by freezing is to prepare frozen beads orpellets comprising the microbial strain. After a suitable fermentation,the liquid is removed from the viable bacteria by a method including butnot limited to centrifugation, ultrafiltration, or sedimentation. Anadditive compound may be added to the bacteria prior to freezing.Suitable additives include but are not limited to, lactose, sucrose,trehalose, maltodextrin, cyclodextrin, spray gum, fish gelatin bloom,and maltitol.

Suitable additives may also serve as cryoprotective agents to improvethe stability of the frozen culture. Cryoprotective agents include, butare not limited to, proteins, protein hydrosolates, carbohydrates, or acompound involved in the biosynthesis of nucleic acids. U.S. Publ. Appl.20070254353. Proteins or protein hydrolysates include but are notlimited to, malt extract, milk powder, whey powder, yeast extract,gluten, collagen, gelatin, elastin, keratin, or albumin. Carbohydratesinclude but are not limited to pentoses (e.g. ribose, xylose), hexoses(e.g. fructose, mannose, sorbose), disaccharides (e.g. sucrose,trehalose, melibiose, lactulose), oligosaccharides (e.g. raffinose),oligofrutoses (e.g. actilight, fribroloses), polysaccharides (e.g.maltodextrins, xanthan gum, pectin, alginate, microcrystallinecellulose, dextran, PEG), and sugar alcohols (sorbitol, manitol). U.S.Publ. Appl. 20070254353.

A foam is defined herein is a composition that is formed by trappingmany gas bubbles in a liquid. Methods pertaining to the formulation andadministration of foams are set forth in U.S. Pat. Nos. 4,112,942,5,652,194, 6,140,355, 6,258,374, and 6,558,043, each of which is hereinspecifically incorporated by reference in its entirety.

A typical foam formulation may, for example, be constructed byintroducing a gas into a gel or aqueous pharmaceutical composition suchthat bubbles of the gas are within the pharmaceutical composition.

A microbial strain formulation can be applied to a surface or simply tothe air using an electrostatic spray apparatus. This apparatus shouldhave a chamber for containing the microbial strain formulation and anopening in fluid connection with the chamber through which the microbialstrain formulation can be dispensed and deposited on a desired surface.The apparatus should allow for electrically charging the microbialstrain formulation. For example, a conductor can be used to connect thechamber to a voltage power source. One of skill in the art would beaware of other suitable devices that can function as such a conductor.

To apply the formulation to a surface or to the air, the formulation isplaced into the chamber of the electrostatic spray apparatus. Themicrobial strain formulation can be pumped into the chamber. When themicrobial strain formulation is placed into the chamber, it contacts theconductor, such as a high-voltage DC electrode, and becomes charged.Once the formulation in the chamber is charged, it carries the samecharge as the conductor. As a result the formulation and conductor repeleach other. This repulsive force discharges the microbial strainformulation through the opening of the nozzle to create streams ofdroplets. Therefore, no additional gas source is required foratomization of the coating formulation. Accordingly, a cloud of highlycharged, highly uniform-sized droplets can be formed.

Since the droplets that are formed carry a charge, when they aredeposited on a grounded surface, they will be guided by theirelectrostatic attraction to the grounded and hence electrically neutralsurface. Since the droplets carry the same electrical charge, they willrepel each other. This repulsion causes the droplets arriving at thesurface to avoid the areas where other droplets have already beendeposited and instead land on areas of the surface that have not beencoated. In this way, an inherently uniform coating is formed.

One example of a suitable nozzle apparatus that can be used in themethod of some embodiments of the invention is an apparatus forelectrohydrodynamic spray-coating that is disclosed in U.S. Pat. No.4,749,125. This apparatus has a metal shim that is placed within thenozzle apparatus to define a plurality of nozzle openings. The metalshim is also connected to a voltage source that allows for the formationof electrically charged droplets of coating formulation. Aerosoldispending system and automated embodiments thereof are furtherdescribed hereinbelow.

Lyophilization—Dry microorganism cultures may be prepared according tomethods which are well known in the art. In addition to constituentspresent in the culture medium, the medium may comprise at least onematrix material with or without other stabilizing substances. Thesematerials may be selected from inorganic salts or buffers, at least oneother compound which is selected from mono-, oligo- and polysaccharides,polyols, polyethers, amino acids, oligo- and polypeptides, milk-derivedcompounds, organic carboxylic acids, mineral compounds, organic carriermaterials such as wheat semolina bran, alginates, DMSO, PVP(polyvinylpyrrolidone), CMC (carboxymethylcellulose), alpha-tocopherol,beta.-carotene and mixtures thereof.

Examples of suitable saccharide carrier components are sucrose,fructose, maltose, dextrose, lactose and maltodextrin. An example of asuitable polyol is glycerol. Examples of suitable amino acids areglutamic acid, aspartic acid and the salts thereof. An example of asuitable peptide carrier is peptone. An example of a milk-derivedcompound is sweet whey powder. Suitable organic carboxylic acids are,for example, citric acid, malic acid and L-ascorbic acid. Examples ofsuitable mineral carriers are montmorillonite and palygorskite.

The microorganism suspension containing the carrier can be dried invarious ways. Suitable drying processes are in principle freeze drying,fluidized-bed drying and, spray-drying. Spray-drying also comprisesmodified spray-drying processes, such as spray-agglomeration oragglomerating spray-drying. The latter process is also known under thename FSD (fluidized spray-dryer) process.

Freeze-drying for preparing dry microorganism cultures according to someembodiments of the present invention can be carried out, for example, onthe basis of the freeze-drying process described in U.S. Pat. No.3,897,307, the contents of which is incorporated completely byreference.

Another drying process contemplated for use according to someembodiments of the present invention is spray-drying. Those methodswhich can be used according to some embodiments of the present inventionare essentially all spray-drying techniques known in the art. Thematerial to be sprayed can, for example, be dried concurrently orcountercurrently; spraying can be carried out by means of asingle-component or multiple-component nozzle or by means of an atomizerwheel.

The drying process according to some embodiments of the presentinvention may be carried out in such a manner that a very low residualmoisture content is present in the dry material. The percentage watercontent is typically from about 2 to 3% by weight. This may be achievedby adding a post-drying step subsequently to the spray-drying step. Thedrying material is, for example, post-dried in a fluidized bed, such asat a temperature in the range of from 15 to 50° C., for a period of, forexample, from 15 minutes to 20 hours. Conditioned compressed air orconditioned nitrogen serves as drying gas.

Instead of the above-described physical post-drying processes, it isalso conceivable to add specific desiccants to the dry material obtainedfrom the spray-drying. Examples of suitable desiccants are inorganicsalts, such as calcium chloride and sodium carbonate, organic polymers,such as the product obtainable under the trade name Kollidion 90 F, andsilicon-dioxide-containing desiccants, such as silica gel, zeolites anddesiccants which are obtainable under the trade name Tixosil 38,Sipernat 22 S or Aerosil 200.

In certain embodiments, the microbial; strain may be refrigerated afterharvesting and concentrating. In certain embodiments, after a suitablefermentation, the liquid is removed from the viable bacteria by a methodincluding but not limited to centrifugation, ultrafiltration, orsedimentation. An additive compound may be added to the bacteria priorto refrigeration. Suitable additives include but are not limited to,lactose, sucrose, trehalose, maltodextrin, cyclodextrin, spray gum, fishgelatin bloom, and maltitol.

Suitable additives may also serve as cryoprotective agents to improvethe stability of the refrigerated culture. Cryoprotective agentsinclude, but are not limited to, proteins, protein hydrosolates,carbohydrates, or a compound involved in the biosynthesis of nucleicacids. U.S. Publ. Appl. 20070254353. Proteins or protein hydrolysatesinclude but are not limited to, malt extract, milk powder, whey powder,yeast extract, gluten, collagen, gelatin, elastin, keratin, or albumin.Carbohydrates include but are not limited to pentoses (e.g. ribose,xylose), hexoses (e.g. fructose, mannose, sorbose), disaccharides (e.g.sucrose, trehalose, melibiose, lactulose), oligosaccharides (e.g.raffinose), oligofrutoses (e.g. actilight, fribroloses), polysaccharides(e.g. maltodextrins, xanthan gum, pectin, alginate, microcrystallinecellulose, dextran, PEG), and sugar alcohols (sorbitol, manitol). U.S.Publ. Appl. 20070254353.

The type of formulation depends on the intended use.

It will be appreciated that the present inventors have identified forthe first time certain activities of the bacterial strain Bacillusamyloliquefaciens. This bacterial strain was found effective and safefor use in the treatment of respiratory tract infections.

As used herein, the term “treating” includes abrogating, substantiallyinhibiting, slowing or reversing the progression of a condition,substantially ameliorating clinical or other symptoms of a condition orsubstantially preventing the appearance of clinical or other symptoms ofa condition.

Thus, according to an aspect of the invention there is provided a methodof controlling a population of pathogenic bacteria and/or fungi in arespiratory system, the method comprising administering to a subject inneed thereof an effective amount of bacteria of the species Bacillusamyloliquefaciens or any composition comprising same such as describedherein, thereby controlling the population of pathogenic bacteria and/orfungi in the respiratory system.

As used herein “Bacillus amyloliquefaciens” refers to a bacterialspecies in the genus Bacillus. It is a gram positive soil bacteriaclosely related to the species Bacillus subtilis. According to aspecific embodiment strains of this bacterial species are as describedherein, e.g., Bacillus amyloliquefaciens 298 and functional homologsthereof.

According to an aspect of the invention there is provided a method ofcontrolling a population of pathogenic bacteria and/or fungi, the methodcomprising providing an effective amount of the isolated bacterialstrain or functional homolog of same or the composition such asdescribed herein, thereby controlling the population of pathogenicbacteria and/or fungi.

As used herein “controlling” refers to preventing or reducing microbialinfections such as a bacterial or fungal infection or inhibiting therate and extent of such infection. Therapeutic treatment is alsocontemplated.

According to a specific embodiment, the controlling is prevention of aninfection.

As described hereinbelow, the present inventors identified the use ofthe bacterial strain as described herein in controlling various speciesof microbes.

Thus, according to some embodiments, the present compositions andmethods are useful in controlling E. coli.

Escherichia coli is a Gram-negative, facultatively anaerobic,rod-shaped, coliform bacterium of the genus Escherichia that is commonlyfound in the lower intestine of warm-blooded organisms. Some E. coliserotypes can cause serious food poisoning in their hosts, and areoccasionally responsible for product recalls due to food contamination.It is most abundant in food and water supply and industrial sites (e.g.,paper production).

According to some additional or alternative embodiments, the presentcompositions and methods are useful in controlling Pseudomonasaeruginosa.

Pseudomonas aeruginosa is a common Gram-negative, rod-shaped bacteriumthat can cause disease in plants and animals, including humans. It isthe most common cause of infections of burn injuries and of the outerear (otitis externa), and is the most frequent colonizer of medicaldevices (e.g., catheters). Pseudomonas can be spread by equipment thatgets contaminated and is not properly cleaned or on the hands ofhealthcare workers. Pseudomonas can cause community-acquired pneumonias,as well as ventilator-associated pneumonias, being one of the mostcommon agents isolated in several studies. One in ten hospital-acquiredinfections is from Pseudomonas. Cystic fibrosis patients are alsopredisposed to P. aeruginosa infection of the lungs. P. aeruginosa mayalso be a common cause of “hot-tub rash” (dermatitis), caused by lack ofproper, periodic attention to water quality. Since these bacteria likemoist environments, such as hot tubs and swimming pools, they can causeskin rash or swimmer's ear. Pseudomonas is also a common cause ofpostoperative infection in radial keratotomy surgery patients. Theorganism is also associated with the skin lesion ecthyma gangrenosum. P.aeruginosa is frequently associated with osteomyelitis involvingpuncture wounds of the foot, believed to result from direct inoculationwith P. aeruginosa via the foam padding found in tennis shoes, withdiabetic patients at a higher risk.

According to some additional or alternative embodiments, the presentcompositions and methods are useful in controlling Bacillus cereus.

Bacillus cereus is a Gram-positive, rod-shaped, aerobic, facultativelyanaerobic, motile, beta hemolytic bacterium commonly found in soil andfood. Some strains are harmful to humans and cause foodborne disease.Bacillus foodborne diseases occur due to survival of the bacterialendospores when food is improperly cooked. Cooking temperatures lessthan or equal to 100° C. (212° F.) allow some B. cereus spores tosurvive. This problem is compounded when food is then improperlyrefrigerated, allowing the endospores to germinate.

According to some additional or alternative embodiments, the presentcompositions and methods are useful in controlling Staphylococcusaureus.

Staphylococcus aureus is a Gram-positive, round-shaped bacterium that isa member of the Firmicutes, and it is a member of the normal flora ofthe body, frequently found in the nose, respiratory tract, and on theskin. It is often positive for catalase and nitrate reduction and is afacultative anaerobe that can grow without the need for oxygen. It is acommon cause of skin infections including abscesses, respiratoryinfections such as sinusitis, and food poisoning. Pathogenic strainsoften promote infections by producing virulence factors such as potentprotein toxins, and the expression of a cell-surface protein that bindsand inactivates antibodies. The emergence of antibiotic-resistantstrains of S. aureus such as methicillin-resistant S. aureus (MRSA) is aworldwide problem in clinical medicine. Despite much research anddevelopment there is no approved vaccine for S. aureus. Spread of S.aureus (including MRSA) generally is through human-to-human contact,although recently some veterinarians have discovered the infection canbe spread through pets. Recently, myriad cases of S. aureus have beenreported in hospitals across America. Transmission of the pathogen isfacilitated in medical settings where healthcare worker hygiene isinsufficient. S. aureus is an incredibly hardy bacterium, as was shownin a study where it survived on polyester for just under three months;polyester is the main material used in hospital privacy curtains. Thebacteria are transported on the hands of healthcare workers, who maypick them up from a seemingly healthy patient carrying a benign orcommensal strain of S. aureus, and then pass it on to the next patientbeing treated. Introduction of the bacteria into the bloodstream canlead to various complications, including endocarditis, meningitis, and,if it is widespread, sepsis.

According to some additional or alternative embodiments, the presentcompositions and methods are useful in controlling SalmonellaTyphimurium.

Salmonella Typhimurium. is a serogroup of a rod-shaped, flagellated,facultative anaerobic, Gram-negative bacterium and a member of the genusSalmonella. It is a serovar that is a serious human pathogen. Theencounter of humans to S. Typhimurium is made via fecal-oral route frominfected individuals or animals to healthy ones, with food as a commonvector. Poor hygiene of patients shedding the organism can lead tosecondary infection, as well as consumption of shellfish from pollutedbodies of water. Most common source of infection, however, are food ofanimal origin and drinking water tainted by urine and feces of infectedindividuals and animals.

According to some additional or alternative embodiments, the presentcompositions and methods are useful in controlling Alternaria alternata.

Alternaria alternata is a fungus which has been recorded causing leafspot and other diseases on over 380 host species of plant. It is anopportunistic pathogen on numerous hosts causing leaf spots, rots andblights on many plant parts. In order to survive, Alternaria alternataneeds a moist warm environment. It is often found in areas with humidclimates, or where there has been significant rainfall. The fungus livesin seeds and seedlings, and is also spread by spores. This diseaseflourishes in dead plants that have been left in gardens over winter.Additionally, when dead infected debris is added to compost pile it canspread to other vegetables throughout the garden.

According to some additional or alternative embodiments, the presentcompositions and methods are useful in controlling Cladosporiumsphaerospermum.

Cladosporium sphaerospermum is a fungus belonging to the genusCladosporium. Cladosporium sphaerospermum is mainly known as a spoilageagent of harvested fruits and vegetables. Cladosporium sphaerospermum isa cosmopolitan fungus that inhabits city buildings and the environmentand because of its airborne nature it can move rapidly betweenlocations. Cladosporium sphaerospermum is also been shown to inhabitpaint films on walls and other surfaces as well as old paintings. Thisfungus is also able to grow on gypsum-based material with and withoutpaint and wallpaper. Plant materials that are affected include citrusleaves on various other decaying plant leaves, on the stems ofherbaceous and woody plants, on fruits and vegetables. The fungus hasalso been reported from wheat-based bakery items.

According to some additional or alternative embodiments, the pathogenicbacteria and/or fungi are airborne pathogens that typically causeinflammation in the respiratory system e.g., nose, throat, sinuses andthe lungs.

Examples of severe infections caused by airborne bacteria include, butare not limited to tuberculosis, pneumonia, and legionellosis.

As mentioned, according to some embodiments, the methods describedherein are directed to controlling a population of pathogenic bacteriaand/or fungi in a respiratory system which may cause a respiratory tractdisease.

For administration by nasal inhalation, the active ingredients for useaccording to some embodiments of the invention are convenientlydelivered in the form of an aerosol spray presentation from apressurized pack or a nebulizer with the use of a suitable propellant,e.g., dichlorodifluoromethane, trichlorofluoromethane,dichloro-tetrafluoroethane or carbon dioxide. In the case of apressurized aerosol, the dosage unit may be determined by providing avalve to deliver a metered amount. Capsules and cartridges of, e.g.,gelatin for use in a dispenser may be formulated containing a powder mixof the compound and a suitable powder base such as lactose or starch.

In one embodiment, the composition according to the present inventionmay be administered in an aerosol, for example by way of a nasal spray,for instance for administration to the respiratory tract.

As used herein the term “respiratory tract disease” refers to diseasesof the upper and/or lower respiratory tracts. The term disease as usedherein is synonymous with the term disorder.

In one embodiment the respiratory tract disease is an upper respiratorytract disease.

Upper respiratory tract diseases include, for example, one or more ofthroat soreness, sneezing, blocked nose, runny nose or a cough is asymptom of one or more of the group consisting of: tonsillitis, otitismedia rhinitis (inflammation of the nasal mucosa); rhinosinusitis orsinusitis (inflammation of the nares and paranasal sinuses, includingfrontal, ethmoid, maxillary, and sphenoid); nasopharyngitis,rhinopharyngitis or the common cold (inflammation of the nares, pharynx,hypopharynx, uvula, and tonsils); pharyngitis (inflammation of thepharynx, hypopharynx, uvula, and tonsils); epiglottitis orsupraglottitis (inflammation of the superior portion of the larynx andupraglottic area); laryngitis (inflammation of the larynx);laryngotracheitis (inflammation of the larynx, trachea, and subglotticarea); and tracheitis (inflammation of the trachea and subglottic area).

In one embodiment the respiratory tract disease is a lower respiratorytract disease.

Lower respiratory tract diseases include, for example, bronchitis, acutebronchitis, pneumonia, lung abscesses.

According to some embodiments, the present teachings are directed atcontrolling pathogenic microbes which include, but are not limited to,Salmonella Typhimurium, Salmonella enterica, Salmonella enteritidis,Clostridium botulinum, Staphylococcus aureus, Campylobacter jejuni,Yersinia enterocolitica and Yersinia pseudotuberculosis, Vibrio choleraeO1, Vibrio cholerae non-O1, Vibrio parahaemolyticus and other Vibriospp., Vibrio vulnificus, Clostridium perfringens, Bacillus cereus,Aeromonas hydrophila, Plesiomonas shigelloides, Shigella spp.,miscellaneous enteric pathogens, and Streptococcus spp.

According to some embodiments the diseases caused by the pathogenicmicrobes include, but are not limited to, staphylococcal infections(caused, for example, by Staphylococcus aureus, Staphylococcusepidermidis, or Staphylococcus saprophyticus), streptococcal infections(caused, for example, by Streptococcus pyogenes, Streptococcuspneumoniae, or Streptococcus agalactiae), enterococcal infections(caused, for example, by Enterococcus faecalis) diphtheria (caused, forexample, by Corynebacterium diptheriae), anthrax (caused, for example,by Bacillus anthracis), listeriosis, gangrene (caused, for example, byClostridium perfringens), tetanus (caused, for example, by Clostridiumtetani), botulism (caused, for example, by Clostridium botulinum), toxicenterocolitis (caused, for example, by Clostridium difficile), bacterialmeningitis (caused, for example, by Neisseria meningitidis), bacteremia(caused, for example, by Neisseria gonorrhoeae), E. coli infections(colibacilliocis), including urinary tract infections and intestinalinfections, shigellosis (caused, for example, by Shigella species),salmonellosis (caused, for example, by Salmonella species), yersiniainfections (caused, for example, by Yersinia pestis, Yersiniapseudotuberculosis, or Yersinia enterocolitica), cholera (caused, forexample, by Vibrio cholerae), campylobacteriosis (caused, for example,by Campylobacter jejuni or Campylobacter fetus), gastritis (caused, forexample, by Helicobacter pylori), pseudomonas infections (caused, forexample, by Pseudomonas aeruginosa or Pseudomonas mallei), Haemophilusinfluenzae type B (HIB) meningitis, HIB acute epiglottitis, or HIBcellulitis (caused, for example, by Haemophilus influenzae), pertussis(caused, for example, by Bordetella pertussis), mycoplasma pneumonia(caused, for example, by Mycoplasma pneumoniae), nongonococcalurethritis (caused, for example, by Ureaplasma urealyticum),legionellosis (caused, for example, by Legionella pneumophila),syphillis (caused, for example, by Treponema pallidum), leptospirosis(caused, for example, by Leptospira interrogans), Lyme borreliosis(caused, for example, by Borrelia burgdorferi), tuberculosis (caused,for example, by Mycobacterium tuberculosis), leprosy (caused, forexample, by Mycobacterium leprae), actinomycosis (caused, for example,by Actinomyces species), nocardiosis (caused, for example, by Nocardiaspecies), chlamydia (caused, for example, by Chlamydia psittaci,Chlamydia trachomatis, or Chlamydia pneumoniae), Rickettsial diseases,including spotted fever (caused, for example, by Rickettsia ricketsii)and Rickettsial pox (caused, for example, by Rickettsia akari), typhus(caused, for example, by Rickettsia prowazekii), brucellosis (caused,for example, by Brucella abortus, Brucella melitens, or Brucella suis),and tularemia (caused, for example, by Francisella tularensis). Diseaseswith similar origins and symptoms are also known to affect animals.

According to a specific embodiment, the controlling is prophylactic(reduces the incidence of infection).

According to a specific embodiment, the controlling is therapeutic(reduces the symptoms and/or duration of infection).

The bacterial strains/species can be administered to subjects in needthereof using methods which are well known in the art.

When used as a medicament, the bacterial strains/species of the presentinvention may be used in any suitable form—whether when alone or whenpresent in a combination with other components or ingredients.

The microorganism of the present invention or composition of the presentinvention may be used in the form of solid or liquid preparations oralternatives thereof. Examples of solid preparations include, but arenot limited to tablets, capsules, dusts, granules and powders which maybe wettable, spray-dried or freeze-dried. Examples of liquidpreparations include, but are not limited to, aqueous, organic oraqueous-organic solutions, suspensions and emulsions.

Suitable examples of forms include one or more of: tablets, pills,capsules, ovules, solutions or suspensions, which may contain flavouringor colouring agents, for immediate-, delayed-, modified-, sustained-,pulsed- or controlled-release applications.

By way of example, if the composition of the present invention is usedin a tablet form—such for use as a functional ingredient—the tablets mayalso contain one or more of: excipients such as microcrystallinecellulose, lactose, sodium citrate, calcium carbonate, dibasic calciumphosphate and glycine; disintegrants such as starch (preferably corn,potato or tapioca starch), sodium starch glycollate, croscarmellosesodium and certain complex silicates; granulation binders such aspolyvinylpyrrolidone, hydroxypropylmethylcellulose (HPMC),hydroxypropylcellulose (HPC), sucrose, gelatin and acacia; lubricatingagents such as magnesium stearate, stearic acid, glyceryl behenate andtalc may be included.

Examples of nutritionally acceptable carriers for use in preparing theforms include, for example, water, salt solutions, alcohol, silicone,waxes, petroleum jelly, vegetable oils, polyethylene glycols, propyleneglycol, liposomes, sugars, gelatin, lactose, amylose, magnesiumstearate, talc, surfactants, silicic acid, viscous paraffin, perfumeoil, fatty acid monoglycerides and diglycerides, petroethral fatty acidesters, hydroxymethyl-cellulose, polyvinylpyrrolidone, and the like.

Exemplary excipients for the forms include lactose, starch, a cellulose,milk sugar or high molecular weight polyethylene glycols.

For aqueous suspensions and/or elixirs, the composition of the presentinvention may be combined with various sweetening or flavouring agents,colouring matter or dyes, with emulsifying and/or suspending agents andwith diluents such as water, propylene glycol and glycerin, andcombinations thereof.

The forms may also include gelatin capsules; fibre capsules, fibretablets etc.; or even beverages.

Further examples of forms are in the form of a cream for example. Forsome aspects the microorganism may be included in pharmaceutical and/orcosmetic creams such as sun creams and/or after-sun creams for example.

In one aspect, the composition according to the present invention may beadministered in an aerosol, for example by way of a nasal spray, forinstance for administration to the respiratory tract.

According to a specific embodiment, the microbial species/strains asdescribed herein are dispensed from an aerosol dispensing device (orsystem).

There are devices known to atomize a liquid and deliver the atomizedliquid into the surrounding air.

According to a specific embodiment the aerosol dispensing device isautomated.

Such an aerosol dispersing device can work on its own as well as inconjunction with an HVAC system.

Reference is now made to FIG. 13 showing a simplified schematic drawingof an example aerosol dispensing device with a replaceable cartridgethat is actuated with compressed air in accordance with some exampleembodiments. An aerosol dispensing device 200 includes a housing 201that may house an air compressor 104 to actuate atomizing a liquid 159contained in a cartridge 150. Pressurized air provided by compressor 104may be delivered through valve 102 and a channel 112, e.g. a tube to aconnector 118. Connector 118 may establish a fluid connection betweencompressor 104, cartridge 150 and an aerosol outlet 129 from whichatomized liquid 125 may be expelled. An atomizer 120 may be integratedin connector 118 or in collar 152 of cartridge 150. Optionally, anadaptor 119 provides a sealed connection between cartridge 150 andconnector 118. Although connector 118 and adaptor 119 are shown as twoseparate elements, it is understood that functionality of these twoelements may be integrated into a single part.

According to some example embodiments, at least one of a cartridge foran aerosol dispensing device and the aerosol dispensing device includesa mechanism for stirring liquid contents of the cartridge. Optionally,liquid content in the cartridge may be stirred continuously orperiodically during use to maintain a substantially constantconcentration of active material over a height of the liquid.

In some example embodiments, device 200 is self-powered with a powersource 108. Alternatively, device 200 may be powered by an externalpower source. In some example embodiments, device 200 includes a userinterface including for example a display 103 and one or more useractuated buttons or knobs 107.

Device 200 may be positioned in an indoor environment. The indoorenvironment may be a public space such as a hospital or a shoppingcenter or may be a personal space such as an office, a home or avehicle. Optionally, device 200 may be configured to direct aerosol 125expelled from channel 129 into airflow ducts of a heating, ventilationand air conditioning (HVAC) system. Optionally, circuit 105 is incommunication or receives input from an HVAC system and is operated incoordination with the HVAC system. Alternatively, device 200 may beoperated independently from an HVAC system and the aerosol may also bedispersed directly into the indoor space, e.g. not through the HVACducts.

One such configuration is described in U.S. Pat. No. 8,986,610 entitled“Apparatus and method for dispersing liquid in aerosol,” the contents ofwhich is incorporated by reference herein, describes a system and methodto deliver an atomized solution to the interior volume of a building orroom utilizing a Venturi effect for the atomization. It is describedthat the solution may contain at least one active material including atleast one of a medicament, probiotic, nutraceutical, or combinationsthereof. The system includes a solution chamber; a Venturi configurationoperatively associated with said solution chamber; an air inletassociated with a pressurized air inlet source; an actuator and asensor. The solution chamber may be in the form of a replaceablecartridge.

In known automated aerosol dispensing devices, the live organism oractive material is typically in the form of a water based solutionstored in a replaceable cartridge. A device with embodiments havingcartridge replacement embodiments is further described hereinbelow.

Reference is now made to FIGS. 14A and 14B showing a simplifiedschematic drawing of an example aerosol dispensing device and an examplereplaceable cartridge respectively and to FIG. 15 showing an examplereplaceable cartridge installed in an example aerosol dispensing deviceall in accordance with some example embodiments. An aerosol dispensingdevice 100 includes a housing 101 that may house an actuator 109configured to actuate atomization of a liquid 159 in a cartridge 150, anoutlet channel 129 from which atomized liquid 125 may be expelled and acircuit 105 configured to control operation of actuator 109. An atomizer120 for creating aerosol 125 based on actuation with actuator 109, maybe integrated as part of actuator 109 or may be integrated in cartridge150. Optionally, actuator 109 is configured to establish fluidconnection with cartridge 150. According to some example embodiments,aerosol dispensing device 100 additionally includes a reader 106configured to read data on a tag 160 included on cartridge 150.

In some example embodiments, device 100 is self-powered with a powersource 108. Alternatively, device 100 may be powered by an externalpower source. In some example embodiments, device 100 includes a userinterface including for example a display 103 and one or more useractuated buttons or knobs 107. Optionally, device 100 additionallyincludes a sensor 117 configured to sense when cartridge 150 isinstalled in device 100. Sensor 117 may for example be an opto-couplersensor that detects a break in a line of sight due to insertion of neck152 into actuator 109. In another example, sensor 117 may be a buttonswitch that is compressed based on insertion of collar 152 into actuator109.

Device 100 may be positioned in an indoor environment. The indoorenvironment may be a public space such as a hospital or a shoppingcenter or may be a personal space such as an office, a home or avehicle. Optionally, device 100 may be configured to direct aerosol 125expelled from channel 129 into airflow ducts of a heating, ventilationand air conditioning (HVAC) system. Optionally, circuit 105 is incommunication or receives input from an HVAC system and is operated incoordination with the HVAC system. Alternatively, device 100 may beoperated independently from an HVAC system and the aerosol may also bedispersed directly into the indoor space, e.g. not through the HVACducts.

According to some example embodiments, liquid 159 may include sensitivematerial such as a pro-biotic, medicament, nutraceutical, orcombinations thereof that may be prone to contamination. The materialwhen contaminated may pose a health hazard. Furthermore, any malicioustampering with cartridge 150 may also lead to a hazardous situation. Forexample an offender may maliciously insert a harmful bacteria or anirritant into cartridge 150. Alternately, an offender may attempt torefill cartridge 150 with unknown or unregulated contents that may notbe suitable or safe in general or for a particular indoor space. Inother examples, a hazardous situation may be created without maliciousintent, for example when a solution in the cartridge has passed itsexpiration date or when a property of the solution has been altered dueto prolonged exposure to humidity or air.

According to some example embodiments, circuit 105 includes safetyverification functionality to verify compatibility, authenticity andsafety of cartridge 150 when it is inserted into housing 101 andoptionally to provide ongoing monitoring while cartridge 150 ismaintained in device 100. The verification may be based on inputreceived from reader 106. In some example embodiments, circuit 105receives data from reader 106 and compares the data received toinformation stored in memory. Optionally, if an identification code readby reader 106 matches an identification code listed in the memory,verification may be established. The memory may be memory included incircuit 105, memory included in a remote server 800 or memory includedin a cloud. Optionally, the information needed to verify authenticationof cartridges may be uploaded by a remote server 800 and circuit 105 mayaccess the information based on wireless communication. According tosome example embodiments, circuit 105 is configured to terminatedispersion or formation of atomized liquid 125 and provide an alert whencartridge 150 cannot be positively verified.

Reader 106 may be configured to scan a code or interrogate a tag 160positioned on cartridge 150, when cartridge 150 is installed in device100 and provide the data to circuit 105. In some examples, reader 106 isor includes a camera or a RFID scanner that is configured to detect datastored on cartridge 150. Preferably, reader 106 is an active reader thatis controlled and powered with circuit 105. In some example embodiments,controller 105 activates reader 106 at a defined frequency, e.g. every5-60 minutes to scan or interrogate tag 160. Additionally oralternatively, controller 105 may activate reader at defined events. Forexample controller 105 may activate reader when power of device 100 isturned on and during installation of cartridge 150 in the device 100. Insome example embodiments communication between reader 106 and tag 160 iswireless or contactless. In other example embodiments, communicationbetween reader 106 and tag 160 is based on electrical contact.

Optionally, cartridge 150 configured for use with device 100 includestag or code 160 with data to verify its compatibility. Tag or code 160may be a barcode, e.g. a one dimensional or two dimensional barcode,maybe in passive RFID tag and may be an active RFID tag. Tag or code 160may be positioned in an inner surface of cartridge 150 that is incontact with fluid 159 or may be positioned on an outer surface ofcartridge 150. According to some example embodiments, tag or code 160may be positioned on cartridge 150 so that it aligns with reader 106while establishing a sealed connection with actuator 109.

In some example embodiments, tag or code 160 includes passive storage.Information tagged or coded on tag or code 160 may include one or moreof the following items: state of a seal on the cartridge, identificationdata, part number of the product, batch number, production date,expiration date, quantity of material in the cartridge, contents of thecartridge and operating instructions.

Optionally, contents 159 of cartridge 150 are sealed with a seal undercap 151 that is configured to be broken in actuator 109 while insertingcartridge 150 into housing 101. Optionally, breaking of the seal altersdata stored in tag or code 160 so that the event may be recorded anddetected by reader 106. Optionally, this information may be used toprevent operating device 100 with cartridges that have been refilled.Cartridge 150 may be in the form of a bottle or may be any containerthat can contain fluid 159 to be dispersed as an aerosol. Typicallycartridge 150 is configured to be replaced after its contents have beenemptied.

In some example embodiments, tag 160 may be an active tag and reader 106may transmit data to tag 160 that may be stored in tag 160. Activestorage may be a microchip with RAM memory in which case a small powersource may be included on cartridge 150. Alternatively, active storagemay be an active RFID.

FIG. 16 shows a simplified schematic drawing of an example aerosoldispensing device including one or more sensors in accordance with someexample embodiments. According to some example embodiments, the aerosoldispensing device 500 includes a regulator configured to regulateactivity of device 500 installed with a cartridge 150. Functionality ofthe regulator may be included in circuit 105. Optionally, device 500includes reader 106 and circuit 105 may regulate activity of device 500based on information received from reader 106, e.g. instruction that maybe specific to liquid 159 contained in the cartridge. Circuit 105 mayadditionally or alternatively regulate activity of device 500 based oninputs from one or more sensors in communication with circuit 105. Insome example embodiment, device 500 includes sensors 128 configured todetect a parameter related to content 159 in cartridge 150. Optionally,sensor 128 is a level sensor for detecting a level of liquid 159 incartridge 150. Optionally, one sensor 128 may be positioned to senseliquid at 1-3 cm from a bottom of cartridge 150 to detect when contentsof cartridge 150 are nearly emptied. In some example embodiments, whencontents of cartridge 150 are nearly emptied, circuit 105 may provide analert on display 103 and may also communicate this information to aremote server 800 in communication with circuit 105. Remote server 800may then alert a service provider or deliver a new cartridge to the siteincluding device 500.

Device 500 may additionally include sensors 127 that may detectenvironmental conditions. Optionally, humidity is detected. In someexample embodiments, temperature is detected. At times, an expirationdate may be adjusted based on the detected environmental conditions. Forexample an expiration date may be shortened in environments with higherhumidity as compared to environments that are more arid. Optionally,frequency or duration of actuation may be adjusted based on outputdetected from one or more of sensors 127, sensors 128 and based on dataread with reader 106.

In some example embodiments, device 500 may be configured to receiveinput from a stand-alone sensor 126 that is remote from device 500.Input may be received based on tethered or wireless connection.Stand-alone sensor 126 may be for example an air quality probe similarto E4000 indoor air quality probe offered by NanoSense, France, athermostat associated with an HVAC, or a humidity sensor. Input fromremote sensors 126 may similarly be used to adjust an expiration date orto adjust frequency or duration of actuation based on the detectedenvironmental conditions.

According to some example embodiments, the aerosol dispensing device 500additionally includes safety verification functionality as describedherein above to verify compatibility, authenticity and safety ofcartridge 150 when it is inserted into device 500 and optionally toprovide ongoing monitoring while cartridge 150 is maintained in device500. In some example embodiments, the safety verification functionalityis based on reader 106 reading data on a tag 160 included on cartridge150 and circuit 105 processing the data.

According to some embodiments the bacterial species/strains as describedherein or compositions comprising same are not to be used in thetreatment of agricultural water (irrigation water), agricultural soilsand agricultural crops.

According to some embodiments, the bacterial species/strains asdescribed herein or compositions comprising same can be used in thetreatment of agricultural water (irrigation water), agricultural soilsand agricultural crops. In still other embodiments, the formulations ofcultured bacteria can be applied in the treatment at food processingfacilities. In the case of food processing facilities, agriculturalwaters and soils, the formulations of cultured bacteria can be appliedprophylactically or as a sanitizing agent following an exposure. Theproduct can be used to treat foods including meat and meat products. Themeat product can generally be any whole, cut, ground or processed meatproduct, including, ground beef (“hamburger”), ground turkey, groundchicken, ground pork, beef sausage, pork sausage, chicken sausage,turkey sausage, hot dogs, bologna, salami, cold cuts, game hens, wholechicken, lamb, ham, pork, cube meat, steaks, roasts, fillets, fish, orliver.

Any type of agricultural produce sold in marketplaces, such as thosederived from plant or fungi, can be treated by the methods andcompositions disclosed herein. Additional types of produce products thatcan be treated by the disclosed antimicrobial compositions include butare not limited to those derived from leaves, stems, fruit, flowers,seeds, roots, and like components that form the plant, as well as thosederived from fungi, including the cap, stem, mycelium and annulus, andlike components that form the fungi.

Any type of surface can be treated with the bacterial strains/species asdescribed herein. Examples of surfaces that may be treated include ofanimate surfaces such, as those of animals or plants, and inanimatesurface, such as food, buildings, furniture, objects and the like.Specific examples of surfaces that the composition could be applied toinclude, but are not limited to the following: meat, grinders,processors, extruders, cutting surfaces, cutting apparatus, blades,seafood, agricultural produce (fruit, vegetables, etc.), nuts, legumes,sprouts, trees, leaves, seeds, bulbs, flowers, animals (livestock andpets), eggs shells, skin, hair, bone, horn, hooves, wool, leather,lawns, fields, soil, floors, walls, countertops, cabinets, toilets,bathtubs, bathrooms (portable and non-portable), sinks, laundryequipment, kitchen appliances (refrigerators, freezers, dishwashers,etc.), heating and refrigeration coils, fans, ceiling fans, heatingsystems, air conditioning system, ventilation systems, internal andexternal ducts for ventilation, heating and air conditioning, tabletops,chairs and sofas, desks, luggage, fabrics, clothing, footwear, sportsequipment, audio/visual equipment, computers, clocks, boxes (cardboard,wood, etc.), books, paper surfaces, garbage/trash receptacles, buildingmaterials, interior and exterior of transportation equipment(automobiles, airplanes, trains, boats, etc.), interior and exterior ofspacecraft and other space facilities, trailers, tires, metal, ceramic,tile, linoleum, carpet, wall paper, painted surfaces, plastic, vinyl,polyvinyl chloride (PVC) and the like, plastic, rubber, glass, hoseline, plumbing (inside and outside), other application machinery,lighting, heating and cooling filaments, ovens, storage containers,bottles, cans, reception areas, milking parlors, food processingfacilities, and the like.

The article of manufacture may be packaged in a form that is appropriateor convenient for shipment, administration, or storage. For example, theproduct can be placed into a hermetically sealed pouch of plastic,paper, metalized plastic, or metal (e.g. aluminum), bottle, cartridgecapsule, plastic bag, or a box. In the article of manufacture eachstrain can be packaged in a separate package or some strains can becombined (e.g., B. subtilis 3 and B. subtilis 281 strains) or allcombined together (composition which comprises all the bacteria).

As used herein the term “about” refers to ±10%.

The terms “comprises”, “comprising”, “includes”, “including”, “having”and their conjugates mean “including but not limited to”.

The term “consisting of” means “including and limited to”.

The term “consisting essentially of” means that the composition, methodor structure may include additional ingredients, steps and/or parts, butonly if the additional ingredients, steps and/or parts do not materiallyalter the basic and novel characteristics of the claimed composition,method or structure.

As used herein, the singular form “a”, “an” and “the” include pluralreferences unless the context clearly dictates otherwise. For example,the term “a compound” or “at least one compound” may include a pluralityof compounds, including mixtures thereof.

Throughout this application, various embodiments of this invention maybe presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to includeany cited numeral (fractional or integral) within the indicated range.The phrases “ranging/ranges between” a first indicate number and asecond indicate number and “ranging/ranges from” a first indicate number“to” a second indicate number are used herein interchangeably and aremeant to include the first and second indicated numbers and all thefractional and integral numerals therebetween.

As used herein the term “method” refers to manners, means, techniquesand procedures for accomplishing a given task including, but not limitedto, those manners, means, techniques and procedures either known to, orreadily developed from known manners, means, techniques and proceduresby practitioners of the chemical, pharmacological, biological,biochemical and medical arts.

When reference is made to particular sequence listings, such referenceis to be understood to also encompass sequences that substantiallycorrespond to its complementary sequence as including minor sequencevariations, resulting from, e.g., sequencing errors, cloning errors, orother alterations resulting in base substitution, base deletion or baseaddition, provided that the frequency of such variations is less than 1in 50 nucleotides, alternatively, less than 1 in 100 nucleotides,alternatively, less than 1 in 200 nucleotides, alternatively, less than1 in 500 nucleotides, alternatively, less than 1 in 1000 nucleotides,alternatively, less than 1 in 5,000 nucleotides, alternatively, lessthan 1 in 10,000 nucleotides.

It is understood that any Sequence Identification Number (SEQ ID NO)disclosed in the instant application can refer to either a DNA sequenceor a RNA sequence, depending on the context where that SEQ ID NO ismentioned, even if that SEQ ID NO is expressed only in a DNA sequenceformat or a RNA sequence format.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination or as suitable in any other describedembodiment of the invention. Certain features described in the contextof various embodiments are not to be considered essential features ofthose embodiments, unless the embodiment is inoperative without thoseelements.

Various embodiments and aspects of the present invention as delineatedhereinabove and as claimed in the claims section below find experimentalsupport in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with theabove descriptions illustrate some embodiments of the invention in a nonlimiting fashion.

Generally, the nomenclature used herein and the laboratory proceduresutilized in the present invention include molecular, biochemical,microbiological and recombinant DNA techniques. Such techniques arethoroughly explained in the literature. See, for example, “MolecularCloning: A laboratory Manual” Sambrook et al., (1989); “CurrentProtocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed.(1994); Ausubel et al., “Current Protocols in Molecular Biology”, JohnWiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide toMolecular Cloning”, John Wiley & Sons, New York (1988); Watson et al.,“Recombinant DNA”, Scientific American Books, New York; Birren et al.(eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, ColdSpring Harbor Laboratory Press, New York (1998); methodologies as setforth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis,J. E., ed. (1994); “Culture of Animal Cells—A Manual of Basic Technique”by Freshney, Wiley-Liss, N. Y. (1994), Third Edition; “Current Protocolsin Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al.(eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange,Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods inCellular Immunology”, W. H. Freeman and Co., New York (1980); availableimmunoassays are extensively described in the patent and scientificliterature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153;3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654;3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219;5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed.(1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J.,eds. (1985); “Transcription and Translation” Hames, B. D., and HigginsS. J., eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986);“Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide toMolecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol.1-317, Academic Press; “PCR Protocols: A Guide To Methods AndApplications”, Academic Press, San Diego, Calif. (1990); Marshak et al.,“Strategies for Protein Purification and Characterization—A LaboratoryCourse Manual” CSHL Press (1996); all of which are incorporated byreference as if fully set forth herein. Other general references areprovided throughout this document. The procedures therein are believedto be well known in the art and are provided for the convenience of thereader. All the information contained therein is incorporated herein byreference.

Example 1 Materials and Methods

Strains

Bacillus strain was isolated from home-made Doenjang using Luria BertaniMiller agar (BD, Difco) agar for plating. Representative colonies werepicked from plates with the highest dilution still showing colonies.After purification, the strain was stored at −80° C. The stock culturewas propagated first in 10 ml LB Miller broth (in 50 ml Falcon steriletube) for 18 hours (rotary shaker, 120 RPM), and then the culture was 1%diluted into a fresh media and was propagated in the same conditions asdescribed previously, before each experiment.

Reference strains were obtained from ATCC (American Type CultureCollection) and KACC (Korean Agricultural Culture Collection) and KCTC(Korea, Collection for Type Cultures).

16S rDNA Sequencing

Pure cultures of Bacillus amyloliquefaciens 298 was grown on LB Milleragar (BD Difco) at 37° C. for 24 hours. The plate was sent to SolgentInc. (Deajun, South Korea) for bi-directional 16S rDNA sequencing using(5′-AGA GTT TGATCMTGG CTC AG-3′, SEQ ID NO: 1) and 1492R (5′-TAC GGY TACCTT GTT ACG ACTT-3′ SEQ ID NO: 2) primers by (Reysenbach, Giver et al.1992). Bi-directional sequencing results were assembled using Codon CodeAligner (Codon Code Corporation, USA) and compared with referencesequences of Bacillus species on the GenBank database(www(dot)ncbidotnlm(dot)nih(dot)gov/Blastn/).

API Test

Specific sugar fermentation pattern was monitored using API 50CHB strips(Biomerieux). The Bacillus strain pellet was prepared using LB Milleragar (BD Difco) at 37° C. for 24 hours and centrifuged 14,000 rpm for 5min. The pellet was suspended using the preparation media in the kit andapplied on different sugars according to the instruction manual.

Hemolysis Test

B. amyloliquefaciens 298 was grown at 37° C. for 18 hours in LB brothand then streaked onto 5% sheep blood agar (Hanil Komed) and incubatedfor 24 h at 37° C. Alpha (α) hemolysis was considered as the partialdecomposition of the hemoglobin of the red blood cells, beta (β)hemolysis as the complete breakdown of the hemoglobin of the red bloodcells observed as a clear zone in the agar plate and gamma (γ) hemolysisas the lack of hemolysis. B. cereus ATCC 27348 was used as a positivecontrol.

Lecithinase Test

B. amyloliquefaciens 298 and B. cereus ATCC 27348 (positive control)were grown at 37° C. for 18 hours in LB Miller broth and streaked outonto egg yolk agar. The plates were incubated for 24 h at 37° C. and theformation of a white precipitate around the colonies was considered aspositive for lecithinase activity (Hong, Huang et al. 2008, Sorokulova,Pinchuk et al. 2008).

Antibiotic Resistance Test

The basic protocol was followed by CLSI recommendation (Jorgensen andTurnidge 2015). Pure cultures of B. amyloliquefaciens 298 werecultivated at 37° C. for 18 hours in LB Miller agar. The agar dilutionmethod was used to assess the minimal inhibitory concentration (MIC) ofthe antibiotics against the strain. A single colony was resuspended inphosphate buffer saline (PBS) 1× and adjusted 0.01 optical density (OD).Ten microliters (1×10⁵ CFU/mL) of strain were inoculated on the platesusing multipin-inoculator and incubated at 37 C for 24 hours. The strainwas considered susceptible when they were inhibited at a concentrationfor a specific antimicrobial equal or lower than the established cut-offvalue and resistant bacterial strain when it was not inhibited at aconcentration of a specific antimicrobial higher than the establishedcut-off value according to the parameters established by the EuropeanFood Safety Authority (EFSA).

Inhalation Infection Test

The animal study was approved by Handong Global University Ethicalcommittee. For the experiment, 40 mice were divided into four groupscomprising negative control, two positive controls. infected withpathogenic microorganisms of Streptococcus pneumoniae ATCC49619 andBacillus cereus ATCC27348 and one group infected with the testedmicroorganism. Potential probiotic B. amyloliquefaciens 298 was infectedat a dose of 1×10⁷ CFU/mouse with pre-treatment of cyclophosphamide toinduce immunocompromised status. The cyclophosphamide was used to deriveimmunocompromised animal model to monitor more emphasized influence ofinfected microorganism so called worst case scenario (Kong, Hellermannet al. 2005).

The B. amyloliquefaciens 298 was grown for 18 hours in LB Miller broth(BD Difco) at 37° C. while S. pneumoniae ATCC49619 was cultured on 5%Sheep blood agar and sub-cultured to Brain Heart Infusion broth (BDDifco) and incubated at 37° C. The bacterial solution was diluted using1×PBS to 1×10⁷ CFU/mouse. The inoculum concentration was determined byenumeration of cultured bacteria on agar plates.

The animal lung infection model was carried out in 4-week-old female ICRmice (Hyo-chang science). The mice were anesthetized during respiratoryinfection (Streptococcus pneumoniae ATCC49619 and Bacillus cereusATCC27348) using 50 μL of bacterial suspension through intranasal route.After 24 h post infection, 2 mice of each group were selected randomlyand sacrificed with diethyl ether for enumeration of viable colonies inlungs. Lungs were extracted and homogenized with Phosphate-bufferedsaline (PBS). Before homogenization, lungs were monitored visually. Thehomogenized lung samples were diluted and spread on 5% Sheep blood agarto enumerate number of pathogens in the lungs. The plates were incubatedfor 18 hours. The rest of the mice were monitored during 1 week tomeasure their survival rates (Ginsberg, Moldawer et al. 1991).

Efficacy Tests

The agar well diffusion assay was performed to evaluate the antagonisticactivity of B. amyloliquefaciens 298 against the growth of pathogenicbacteria including Escherichia coli ATCC 22922, Pseudomonas aeruginosa,B. cereus ATCC 27348, Staphylococcus aureus ATCC 11335, SalmonellaTyphimurium ATCC 14028 and Listeria innocua ATCC 3586. The antagonisticactivity of B. amyloliquefaciens 298 was also verified against moldssuch as Alternaria alternata (Fries) Keissler (ATCC® MYA-4642™),Cladosporium sphaerospermum Penzig (ATCC® MYA-4645™) and Penicilliumchrysogenum Thom (ATCC® MYA-4644™). Brain Heart Infusion (BHI) Agar wasused for the antagonism against pathogenic microorganisms while thePotato Dextrose Agar (PDA) was used for evaluation against molds.Reference pathogens were prepared using BHI broth at 37° C. for 18 hourswhile B. amyloliquefaciens 298 was grown using LB broth at 37° C. for 18hours. Molds were prepared using PDA at 25° C. with 85% HR for 7 days.Mold spores, pathogens and B. amyloliquefaciens 298 were harvested andresuspended in PBS. Pathogens and B. amyloliquefaciens 298 were adjustedto an optical density of 0.2 and 100 uL of pathogen suspended in PBS wasspread on BHI agar plates. The same amount of mold spore suspension wasinoculated on PDA. Wells were made in all the plates and 20 μL of B.amyloliquefaciens 298 suspensions were inoculated in the wells while theBHI plates were incubated at 37° C. for 24 hours and PDA plates at 25°C. for 72 hours. The inhibition of pathogens and molds was observed as aclear zone around the bacillus strain inoculated wells and 10% hydrogenperoxide served as a positive control.

16S rDNA Sequence

The identity of the strain was confirmed as B. subtilis according to theNational Center for Biotechnology Information (NCBI) database accordingto the 16S-rRNA (SEQ ID NO: 3) sequencing result.

Complete Genome Sequence

The complete genome sequence of B. amyloliquefaciens 298 was generatedusing the PacBio RS platform with single-molecule real-time (SMRT)sequencing at Theragenetex (Seoul, South Korea). Annotations wereperformed by merging the results obtained from the Rapid Annotationsusing Subsystems Technology (RAST) server, Glimmer 3.02 modelingsoftware, tRNAscan-SE 2.0, and RNAmmer 1.2. In addition, the contigswere searched against the KEGG, UniProt, and Clusters of OrthologousGroups (COG) databases to annotate the gene description. The results areshown in SEQ ID NO: 4.

Metabolite Analysis

Total protein was extracted from growth media of B. amyloliquefaciens298 after 18 hours at 37° C. incubation to evaluate the secretedmetabolites of B. amyloliquefaciens 298. A stock solution was prepareddissolving 500 g of Trichloroacetic acid (TCA) into 350 ml of distilledwater. 1 volume of TCA stock solution was added to 4 volumes of B.amyloliquefaciens 298 growth media and incubated at 4° C. for 10 min.The tube was centrifuged at 14,000 rpm for 5 min and supernatant wasremoved to concentrate the protein pellet. The pellet was washed with200 μl cold acetone and again concentrated by 14,000 rpm centrifugationfor 5 min. This step was repeated for three times and the pellet wassent to be analyzed using LC-LTQ-Orbitrap at Technopark Biocenter(Pohang, South Korea). The raw data was analyzed using UniProt databaseto match predicted proteins from the growth media of B.amyloliquefaciens 298.

Example 1A In-Vitro Safety Evaluation of Lecithinase and HemolysisActivity

B. amyloliquefaciens 298 did not show lecithinase activity observed asthe absence of a white precipitate around the Bacillus colonies and allB. amyloliquefaciens 298 showed negative reaction for hemolysis as well.

TABLE 1 Lecithinase and hemolysis activity of B. amyloliquefaciens 298and B. cereus ATCC 27348. Lecithinase Hemolysis Strain activity activityBacillus amyloliquefaciens 298 Negative Gamma Bacillus cereus ATCC 27348Positive Beta (positive control)

Example 1B In-Vitro Evaluation of Antibiotic Resistance

The agar dilution was used to evaluate the minimal inhibitoryconcentration (MIC) of antibiotics. B. amyloliquefaciens 298 was foundto be sensitive to erythromycin, gentamicin, tetracycline, streptomycin,vancomycin, chloramphenicol, kanamycin and clindamycin according to theEuropean Food Safety Authority MIC breakpoints for Bacillus species. Thedetermined MIC values are clearly below or equal to the EFSA breakpointvalues (Table 2).

TABLE 2 Minimum inhibitory concentrations (MIC) of B. amyloliquefaciens298. Antibiotic resistance test Minimum inhibitory concentration (mg/L)of antibiotics Strain Ery Gen Tet Str Van Chl Kan Cli B.amyloliquefaciens 298 ≤0.125 ≤2 ≤0.125 8 0.25 ≤4 ≤4 0.5 EFSA breakpoint4 4 8 8 4 8 8 4 Ery: Erythromycin; Gen: Gentamicin; Tet: Tetracycline;Str: Streptomycin; Vm: Vancomycin; Chl: Chloramphenicol; Kan: Kanamycin;Cli: Clindamycin.

Example 1C Respiratory Tract Infection Test

The survival rate after respiratory tract infection of B.amyloliquefaciens 298 was 100% while the positive control of pathogenicbacteria infected groups including S. pneumoniae and B. cereus showed100% mortality after 24 hours (FIG. 1). Lung pictures were taken andshowed strong damage in pathogen infected positive groups while lung ofB. amyloliquefaciens 298 infected groups showed similar lung status asnegative control group (FIG. 2) and any colony of Bacillus was foundfrom the homogenized lung of B. amyloliquefaciens 298 infected group(data not shown). These data demonstrate that B. amyloliquefaciens 298does not infect lung probably due to lack of colonization in the lung.

Example 1D Efficacy Tests

The antagonism test results of B. amyloliquefaciens 298 showed inhibitedgrowth of E. coli ATCC 22922, P. aeruginosa, B. cereus ATCC 27348 and S.Typhimurium ATCC 14028 at different degrees (FIG. 3 and Table 3).

TABLE 3 Antagonistic activity of Bacillus amyloliquefaciens 298 againstpathogens. B. Pathogens amyloliquefaciens 298 Escherichia coli ATCC22922 2 Pseudomonas aeruginosa 1 Bacillus cereus ATCC 27348 2Staphylococcus aureus ATCC 11335 1 Salmonella Typhimurium ATCC 14028 2Listeria innocua ATCC 3586 NA NA: No antagonism was observed

B. amyloliquefaciens 298 antagonism against mold indicates positiveantagonism against Alternaria alternata (Fries) Keissler (ATCC®MYA-4642™) and Cladosporium sphaerospermum Penzig (ATCC® MYA-4645™) atvariable level (Table 4). The inhibition of the mold growth is evidentlyexpressed as a clear zone around the wells inoculated with the B.amyloliquefaciens 298 (FIG. 4). Penicillium chrysogenum Thom (ATCC®MYA-4644™) was not inhibited at all for any of the strains used on thisexperiment, however the mycelium color around the well inoculated withB. amyloliquefaciens 298 show and slightly decrease in the intensity(data not shown) from green to white.

TABLE 4 Antifungal activity of Bacillus amyloliquefaciens 298 againstmolds. Inhibition zone (mm) Alternaria alternata CladosporiumPenicillium (Fries) sphaerospermum chrysogenum Keissler Penzig Thom(ATCC (ATCC (ATCC Strain MYA-4642) MYA-4645) MYA-4644) Bacillus 6  6 NAamyloliquefaciens 298 Hydrogen peroxide 10% 8 12 10 NA: No antagonismwas observed

Example 1E Taxonomic Identification

The identity of the strain was confirmed as B. subtilis according to theNational Center for Biotechnology Information (NCBI) database. APIresults were monitored for further identification of physiologicalcharacteristics.

Example 1F Complete Genome Sequence

A Single run of PacBio provided total number of 151,771 reads whichcomprises in total of 1,368,609,189 bases. Raw data was assembled usingCanu v1.6 and single contig was produced in size of 3,928,316 base pairs(Separate attached text file of “Bacillus amyloliquefaciens 298.fasta”).Total number of genes were 3,854 (3,740 coding sequences) and 3,044annotated genes were found which calculated as 81.39% of total genes(gene annotations are listed in Table 5 below).

Lengthy table referenced here US20200405781A1-20201231-T00001 Pleaserefer to the end of the specification for access instructions.

Example 2 Materials and Methods

Strains

Bacillus strains were isolated from home-made Doenjang using LuriaBertani Miller agar (BD, Difco) agar for plating. Representativecolonies were picked from plates with the highest dilution still showingcolonies. After purification, the strains were stored at −80° C. Beforeeach experiment, the stock culture was cultured in 10 ml LB Miller broth(BD, Difco) in 50 ml falcon sterile tubes for 18 hours at 37° C. in ashaking incubator (rotatory, 120 RPM), the tubes were located in a slopeposition at an angle of ca80° relative to the vertical line. Then 1%diluted to fresh media (and grown in the same conditions). The culturewas then streaked on LB Miller agar (BD, Difco) and incubated for 18hours. Representative colony was picked and cultured on LB Miller broth(BD, Difco) at 37° C. in a shaking incubator (rotatory, 120 RPMaccording to the time indicated at each test. Reference strains wereobtained from ATCC (American Type Culture Collection) and KACC (KoreanAgricultural Culture Collection) and KCTC (Korea, Collection for TypeCultures).

16S rDNA Sequencing

Pure cultures of Bacillus subtilis 3 were grown on LB Miller agar (BDDifco) at 37° C. for 24 hours. The plate was sent to Solgent Inc.(Deajun, South Korea) for bi-directional 16S rDNA sequencing using(5′-AGA GTT TGATCMTGG CTC AG-3′, SEQ ID NO: 1) and 1492R (5′-TAC GGY TACCTT GTT ACG ACTT-3′, SEQ ID NO: 2) primers by (Reysenbach, Giver et al.1992). Bi-directional sequencing results were assembled using Codon CodeAligner (Codon Code Corporation, USA) and compared with referencesequences of Bacillus species on the GenBank database(www(dot)ncbi(dot)nlm(dot)nih(dot)gov/Blastn/).

API Test

Specific sugar fermentation pattern was monitored using API 50CHB strips(Biomerieux). The Bacillus strain pellet was prepared using LB Milleragar (BD Difco) at 37° C. for 24 hours and centrifuged 14,000 rpm for 5min. The pellet was suspended using the preparation media in the kit andapplied on different sugars according to the instruction manual.

Hemolysis Test

B. subtilis 3 was grown at 37° C. for 18 hours in LB broth and thenstreaked onto 5% sheep blood agar (Hanil Komed) and incubated for 24 hat 37° C. Alpha (α) hemolysis was considered as the partialdecomposition of the hemoglobin of the red blood cells, beta (β)hemolysis as the complete breakdown of the hemoglobin of the red bloodcells observed as a clear zone in the agar plate and gamma (γ) hemolysisas the lack of hemolysis. B. cereus ATCC 27348 was used as a positivecontrol.

Lecithinase Test

B. subtilis 3 and B. cereus ATCC 27348 (positive control) were grown at37° C. for 18 hours in LB Miller broth and streaked out onto egg yolkagar. The plates were incubated for 24 h at 37° C. and the formation ofa white precipitate around the colonies was considered as positive forlecithinase activity (Hong, Huang et al. 2008, Sorokulova, Pinchuk etal. 2008).

Antibiotic Resistance Test

The basic protocol was followed by CLSI recommendation (Jorgensen andTurnidge 2015). Pure cultures of B. subtilis 3 were cultivated at 37° C.for 18 hours in LB Miller agar. The agar dilution method was used toassess the minimal inhibitory concentration (MIC) of the strain againstantibiotics. A single colony was resuspended in phosphate buffer saline(PBS) 1× and adjusted 0.01 optical density (OD). Ten microliters (1×10⁵CFU/mL) of strain were inoculated on the plates usingmultipin-inoculator and incubated at 37° C. for 24 hours. The strain wasconsidered susceptible when they were inhibited at a concentration for aspecific antimicrobial equal or lower than the established cut-off valueand resistant bacterial strain when it was not inhibited at aconcentration of a specific antimicrobial higher than the establishedcut-off value according to the parameters established by the EuropeanFood Safety Authority (EFSA).

Inhalation Infection Test

The animal study was approved by Handong Global University Ethicalcommittee. For the experiment, 40 mice were divided into four groupscomprising negative control, two positive controls infected withpathogenic microorganisms of Streptococcus pneumoniae ATCC49619 andBacillus cereus ATCC27348. Potential probiotic B. subtilis 3 wasinfected in dose of 1×10⁷ CFU/mouse with pre-treatment ofcyclophosphamide to induce immunocompromised status. Thecyclophosphamide was used to derive immunocompromised animal model tomonitor more emphasized influence of infected microorganims so calledworst case scenario (Kong, Hellermann et al. 2005). The Bacillus strainwas grown for 18 hours in LB Miller broth (BD Difco) at 37° C. while S.pneumoniae ATCC49619 was cultured on 5% Sheep blood agar and subculturedto Brain Heart Infusion broth (BD Difco) and incubated at 37° C. Thebacterial solution was diluted using 1×PBS to 1×10⁷ CFU/mouse. Theinoculum concentration was determined by enumeration of culturedbacteria on agar plates.

The animal lung infection model was carried out in 4-week-old female ICRmice (Hyo-chang science). The mice were anesthetized during respiratoryinfection using 50 μL of bacterial suspension through intranasal route.After 24 h post infection, 2 mice of each group were selected randomlyand sacrificed with diethyl ether for enumeration of viable colonies inlungs. Lungs were extracted and homogenized with Phophate-bufferedsaline (PBS). Before homogenization, lungs were monitored visually. Thehomogenized lung samples were diluted and spread on 5% Sheep blood agarto enumerate number of pathogens in the lungs. The plates were incubatedfor 18 hours. The rest of the mice were monitored during 1 week tomeasure their survival rates (Ginsberg, Moldawer et al. 1991).

Efficacy Tests

The agar well diffusion assay was performed to evaluate the antagonisticactivity of B. subtilis 3 against the growth of pathogenic bacteriaincluding Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC27853, B. cereus ATCC 27348, Staphylococcus aureus ATCC 6538, SalmonellaTyphymurium ATCC 14028 and Listeria inocua ATCC 33090. The antagonisticactivity of B. subtilis 3 was also verified against molds such asAlternaria alternata (Fries) Keissler (ATCC® MYA-4642™), Cladosporiumsphaerospermum Penzig (ATCC® MYA-4645™) and Penicillium chrysogenum Thom(ATCC® MYA-4644™). Brain Heart Infusion (BHI) Agar was used for theantagonism against pathogenic microorganisms while the Potato DextroseAgar (PDA) was used for evaluation against molds. Reference pathogenswere prepared using BHI broth 37° C. for 18 hours, while B. subtilis 3was grown using LB broth at 37° C. for 18 hours. Molds were preparedusing PDA at 25° C. with 85% HR for 7 days. Mold spores, pathogens andB. subtilis 3 were harvested and resuspended in PBS. Pathogens and B.subtilis 3 was adjusted at optical density of 0.2 and 100 μL of pathogensuspended in PBS was spreaded on BHI agar plates. The same amount ofmold spore suspension was inoculated on PDA. Wells were made in all theplates and 20 μL of B. subtilis 3 suspensions were inoculated in theholes while the BHI plates were incubated at 37° C. for 24 hours and PDAplates at 25° C. for 72 hours. The inhibition of pathogens and moldswere observed as a clear zone around the bacillus strain inncoulatedwells and 10% hydrogen peroxide was served as a positive control.

Complete Genome Sequence

The complete genome sequence of B. subtilis 3 was generated using thePacBio RS platform with single-molecule real-time (SMRT) sequencing atTheragenetex (Seoul, South Korea). Annotations were performed by mergingthe results obtained from the Rapid Annotations were performed bymerging the results obtained from the Papid Annotaions using SubsystemsTechnology (RAST) server, Glimmer 3.02 modeling software, tRNAscan-SE2.0, and RNAmmer 1.2. In addition, the contigs were searched against theKEGG, UniProt, and Clusters of Orthologous Groups (COG) databses toannotate the gene description.

Metabolite Analysis

Total protein was extracted from growth media of B. subtilis 3 after 18hours at 37° C. incubation to evaluate metabolite of B. subtilis 3.Stock solution was prepared dissolving 500 g of Trichloroacetic acid(TCA) into 350 ml of distilled water. 1 volume of TCA stock solution wasadded to 4 volumes of B. subtilis 3 growth media and incubated at 4° C.for 10 min. Tube was centrifuged at 14,000 rpm for 5 min and supernatantwas removed to concentrate protein pellet. The pellet was washed with200 μL of cold acetone and again concentrated by 14,000 rpmcentrifugation for 5 min. This step was repeated three times and thepellet was sent to be analyzed using LC-LTQ-Orbitrap at TechnoparkBiocenter (Pohang, South Korea). The raw data was analyzed using UniProtdatabase to match predicted proteins from the growth media of B.subtilis 3.

Example 2A In-Vitro Safety Evaluation of Lecithinase and HemolysisActivity

B. subtilis 3 did not show lecithinase activity observed as the absenceof a white precipitate around the Bacillus colonies and B. subtilis 3showed negative reaction for hemolysis as well.

TABLE 6 Lecithinase and hemolysis activity of B. subtilis 3 and B.cereus ATCC 27348. Lecithinase Hemolysis Strain activity activityBacillus subtilis 3 Negative Gamma Bacillus cereus ATCC Positive Beta27348 (positive control)

Example 2B In-Vitro Evaluation of Antibiotic Resistance

The agar dilution was used to evaluate the minimal inhibitoryconcentration (MIC) of antibiotics. B. subtilis 3 was found to besensitive to erythromycin, gentamicin, tetracycline, streptomycin,vancomycin, chloramphenicol, kanamycin and clindamycin according to theEuropean Food Safety Authority MIC breakpoints for Bacillus species. Thedetermined MIC values are clearly below or equal to the EFSA breakpointvalues (Table 2).

TABLE 7 Minimum inhibitory concentrations (MIC) of B. subtilis 3.Antibiotic resistance test Minimum inhibitory concentration (mg/L) ofantibiotics Strain Ery Gen Tet Str Van Chl Kan Cli B. subtilis 3 ≤2 ≤2≤4 8 ≤2 ≤4 ≤4 4 EFSA breakpoint 4 4 8 8 4 8 8 4 Ery: Erythromycin; Gen:Gentamicin; Tet: Tetracycline; Str: Streptomycin; Vm: Vancomycin; Chl:Chloramphenicol; Kan: Kanamycin; Cli: Clindamycin.

Example 2C Respiratory Tract Infection Test

The survival rate after respiratory tract infection of three candidatesof B. subtilis 3 was 100% while the positive control of pathogenicbacteria infected groups including S. pneumoniae and B. cereus showed100% mortality after 24 hours (FIG. 5). All lung pictures were taken andshowed strong damage in pathogen infected positive groups, while lung ofB. subtilis 3 infected groups showed similar lung status as negativecontrol group (FIG. 6) and no colony of Bacillus was found from thehomogenized lung of B. subtilis 3 infected group (data not shown).

Example 2D Efficacy Tests

The antagonism test results of B. subtilis 3 against pathogenic bacteriaindicate that B. subtilis 3 reduce the growth of E. coli ATCC 22922, S.aureus ATCC 11335 and L. inocua ATCC 3586 at various levels (FIG. 7).

TABLE 8 Antagonistic activity of Bacillus subtilis 3 against pathogens.Pathogens B. subtilis 3 Escherichia coli ATCC 25922 1 Pseudomonasaeruginosa ATCC 27853 NA Bacillus cereus ATCC 27348 NA Staphylococcusaureus ATCC 6538 1 Salmonella Typhmurium ATCC 14028 NA Listeria inocuaATCC 33090 2 NA: No antagonism was observed

B. subtilis 3 antagonism against mold indicate positive antagonismagainst Alternaria alternata (Fries) Keissler (ATCC® MYA-4642™) andCladosporium sphaerospermum Penzig (ATCC® MYA-4645™) at variable level(Table 4). The inhibition of the mold growth is evidently expressed as aclear zone around the wells inoculated with the B. subtilis 3 (FIG. 8).Penicillium chrysogenum Thom (ATCC® MYA4644™) was not inhibited at allfor any of the strains used on this experiment.

TABLE 9 Antifungal activity of Bacillus subtilis 3 against molds.Inhibition zone (mm) Alternaria alternata Cladosporium Penicillium(Fries) sphaerospermum chrysogenum Keissler Penzig Thom (ATCC (ATCC(ATCC Strain MYA-4642) MYA-4645) MYA-4644) Bacillus 2  4 NA subtilis 3Hydrogen 8 12 10 peroxide 10% NA: No antagonism was observed

Example 2E Taxonomic Identification

The identity of the strain was confirmed as B. subtilis according to theNational Center for Biotechnology Information (NCBI) database. APIresults were monitored for further identification of physiologicalcharacteristics.

Example 2F 16S rRNA

The identity of the strain having the 16S rRNA sequence as set forth inSEQ ID NO: 5 was confirmed as B. subtilis, according to the NationalCenter for Biotechnology Information (NCBI) database.

Example 2G Complete Genome Sequence

Single run of PacBio provided total number of 187,256 reads whichcomprises in total of 1,717,197,946 bases. Raw data was assembled usingCanu v1.6 and single contig was produced in size of 4,096,210 base pairs(Separate attached text file of “Bacillus subtilis 3.fasta”). Totalnumber of genes were 4,338 (4,220 coding sequences) and 3,387 annotatedgenes were found which calculated as 80.26% of total genes.

Lengthy table referenced here US20200405781A1-20201231-T00002 Pleaserefer to the end of the specification for access instructions.

Example 3 Materials and Methods

Strains

Bacillus strains were isolated from home-made Doenjang using LuriaBertani Miller agar (BD, Difco) agar for plating. Representativecolonies were picked from plates with the highest dilution still showingcolonies. After purification, the strains were stored at −80° C. Beforeeach experiment, the stock culture was cultured in 10 ml LB Miller broth(BD, Difco) in 50 ml falcon sterile tubes for 18 hours at 37° C. in ashaking incubator (rotatory, 120 RPM), the tubes were located in a slopeposition at an angle of ca80° relative to the vertical line. Then 1%diluted to fresh media (and grown in the same conditions). The culturewas then streaked on LB Miller agar (BD, Difco) and incubated for 18hours. Representative colony was picked and cultured on LB Miller broth(BD, Difco) at 37° C. in a shaking incubator (rotatory, 120 RPMaccording to the time indicated at each test). Reference strains wereobtained from ATCC (American Type Culture Collection) and KACC (KoreanAgricultural Culture Collection) and KCTC (Korea, Collection for TypeCultures).

16S rDNA Sequencing

Pure cultures of Bacillus subtilis 281 were grown on LB Miller agar (BDDifco) at 37° C. for 24 hours. The plate was sent to Solgent Inc.(Deajun, South Korea) for bi-directional 16S rDNA sequencing using(5′-AGA GTT TGATCMTGG CTC AG-3′, SEQ ID NO: 1) and 1492R (5′-TAC GGY TACCTT GTT ACG ACTT-3′ SEQ ID NO: 2) primers by (Reysenbach, Giver et al.1992). Bi-directional sequencing results were assembled using Codon CodeAligner (Codon Code Corporation, USA) and compared with referencesequences of Bacillus species on the GenBank database(www(dot)ncbi(dot)nlm(dot)nihdotgov/Blastn/).

API Test

Specific sugar fermentation pattern was monitored using API 50CHB strips(Biomerieux). The Bacillus strain pellet was prepared using LB Milleragar (BD Difco) at 37° C. for 24 hours and centrifuged 14,000 rpm for 5min. The pellet was suspended using the preparation media in the kit andapplied on different sugars according to the instruction manual.

Hemolysis Test

Bacillus subtilis 281 was grown at 37° C. for 18 hours in LB broth andthen streaked onto 5% sheep blood agar (Hanil Komed) and incubated for24 h at 37° C. Alpha (α) hemolysis was considered as the partialdecomposition of the hemoglobin of the red blood cells, beta (β)hemolysis as the complete breakdown of the hemoglobin of the red bloodcells observed as a clear zone in the agar plate and gamma (γ) hemolysisas the lack of hemolysis. B. cereus ATCC 27348 was used as a positivecontrol.

Lecithinase Test

Bacillus subtilis 2818 and B. cereus ATCC 27348 (positive control) weregrown at 37° C. for 18 hours in LB Miller broth and streaked out ontoegg yolk agar. The plates were incubated for 24 h at 37° C. and theformation of a white precipitate around the colonies was considered aspositive for lecithinase activity (Hong, Huang et al. 2008, Sorokulova,Pinchuk et al. 2008).

Antibiotic Resistance Test

The basic protocol was followed by CLSI recommendation (Jorgensen andTurnidge 2015). Pure cultures of Bacillus subtilis 281 were cultivatedat 37° C. for 18 hours in LB Miller agar. The agar dilution method wasused to assess the minimal inhibitory concentration (MIC) of theantibiotics against the strain. A single colony was resuspended inphosphate buffer saline (PBS) 1× and adjusted to 0.01 optical density(OD). Ten microliters (1×10⁵ CFU/mL) of strain were inoculated on theplates using multipin-inoculator and incubated at 37 C for 24 hours. Thestrain was considered susceptible when they were inhibited at aconcentration for a specific antimicrobial equal or lower than theestablished cut-off value and resistant bacterial strain when it was notinhibited at a concentration of a specific antimicrobial higher than theestablished cut-off value according to the parameters established by theEuropean Food Safety Authority (EFSA).

Inhalation Infection Test

The animal study was approved by Handong Global University Ethicalcommittee. For the experiment, 40 mice were divided into four groupscomprising negative control, two positive controls infected withpathogenic microorganisms of Streptococcus pneumoniae ATCC49619 andBacillus cereus ATCC27348 and one group infected with the testedmicroorganism. Potential probiotic Bacillus subtilis 281 was infected ata dose of 1×10⁷ CFU/mouse with pre-treatment of cyclophosphamide toinduce immunocompromised status. The cyclophosphamide was used to derivean immunocompromised animal model in order to monitor more pronouncedinfluence of the infected microorganism as a so called worst casescenario (Kong, Hellermann et al. 2005).

The Bacillus subtilis 281 was grown for 18 hours in LB Miller broth (BDDifco) at 37° C. while S. pneumoniae ATCC49619 was cultured on 5% Sheepblood agar and sub-cultured in Brain Heart Infusion broth (BD Difco) andincubated at 37° C. The bacterial solution was diluted using 1×PBS to1×10⁷ CFU/mouse. The inoculum concentration was determined byenumeration of cultured bacteria on agar plates.

The animal lung infection model was carried out in 4-week-old female ICRmice (Hyo-chang science). The mice were anesthetized during respiratoryinfection using 50 μL of bacterial suspension through the intranasalroute. After 24 h post infection, 2 mice of each group were selectedrandomly and sacrificed with diethyl ether for enumeration of viablecolonies in lungs. Lungs were extracted and homogenized withphosphate-buffered saline (PBS). Before homogenization, lungs weremonitored visually. The homogenized lung samples were diluted and spreadon 5% Sheep blood agar to enumerate number of pathogens in the lungs.The plates were incubated for 18 h. The rest of mice were monitoredduring 1 week to measure their survival rates (Ginsberg, Moldawer et al.1991).

Efficacy Tests

The agar well diffusion assay was performed to evaluate the antagonisticactivity of B. subtilis 281 against the growth of pathogenic bacteriaincluding Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC27853, B. cereus ATCC 27348, Staphylococcus aureus ATCC 6538, SalmonellaTyphimurium ATCC 14028 and Listeria innocua ATCC 33090. The antagonisticactivity of B. subtilis 281 was also verified against molds such asAlternaria alternata (Fries) Keissler (ATCC® MYA-4642™), Cladosporiumsphaerospermum Penzig (ATCC® MYA-4645™) and Penicillium chrysogenum Thom(ATCC® MYA-4644™). Brain Heart Infusion (BHI) Agar was used for theantagonism against pathogenic microorganisms while the Potato DextroseAgar (PDA) was used for evaluation against molds. Reference pathogenswere prepared using BHI broth 37° C. for 18 h while B. subtilis 281 wasgrown using LB broth at 37° C. for 18 h. Molds were prepared using PDAat 25° C. with 85% HR for 7 days. Mold spores, pathogens and B. subtilis281 were harvested and resuspended in PBS. Pathogens and B. subtilis 281was adjusted at optical density of 0.2 and 100 μL of pathogen suspendedin PBS was spread on BHI agar plates. The same amount of mold sporesuspension was inoculated on PDA. Wells were made in all the plates and20 μL of B. subtilis 281 suspensions were inoculated in the holes whilethe BHI plates were incubated at 37° C. for 24 h and PDA plates at 25°C. for 72 h. The inhibition of pathogens and molds were observed as aclear zone around the bacillus strain innoulated wells and 10% hydrogenperoxide served as a positive control.

Complete Genome Sequence

The complete genome sequence of B. subtilis 281 was generated using thePacBio RS platform with single-molecule real-time (SMRT) sequencing atTheragenetex (Seoul, South Korea). Annotations were performed by mergingthe results obtained from the Rapid Annotations were performed bymerging the results obtained from the Papid Annotaions using SubsystemsTechnology (RAST) server, Glimmer 3.02 modeling software, tRNAscan-SE2.0, and RNAmmer 1.2. In addition, the contigs were searched against theKEGG, UniProt, and Clusters of Orthologous Groups (COG) databases toannotate the gene description.

Metabolite Analysis

Total protein was extracted from growth media of B. subtilis 281 after18 h at 37° C. incubation to evaluate the metabolites of B. subtilis281. Stock solution was prepared by dissolving 500 g of Trichloroaceticacid (TCA) into 350 mL of distilled water. 1 volume of TCA stocksolution was added to 4 volume of B. subtilis 281 growth media andincubated at 4° C. for 10 min. Tube was centrifuged at 14,000 rpm for 5min and supernatant was removed to concentrate protein pellet. Thepellet was washed with 200 μL of cold acetone and again concentrated by14,000 rpm centrifugation for 5 min. This step was repeated for threetimes and the pellet was sent to be analyzed using LC-LTQ-Orbitrap atTechnopark Biocenter (Pohang, South Korea). The raw data was analyzedusing UniProt database to match predicted proteins from the growth mediaof B. subtilis 281.

Example 3A In-Vitro Safety Evaluation of Lecithinase and HemolysisActivity

B. subtilis 281 did not show lecithinase activity observed as theabsence of white precipitation around the Bacillus colonies and all B.subtilis 281 showed negative reaction for hemolysis as well.

TABLE 11 Lecithinase and hemolysis activity of B. subtilis 281 and B.cereus ATCC 27348. Lecithinase Hemolysis Strain activity activity B.subtilis 281 Negative Gamma Bacillus cereus ATCC Positive Beta 27348(positive control)

Example 3B In-Vitro Evaluation of Antibiotic Resistance

The agar dilution was used to evaluate the minimal inhibitoryconcentration (MIC) of antibiotics. B. subtilis 281 was found to besensitive to erythromycin, gentamicin, tetracycline, streptomycin,vancomycin, chloramphenicol, kanamycin and clindamycin according to theEuropean Food Safety Authority MIC breakpoints for Bacillus species. Thedetermined MIC values are clearly below or equal to the EFSA breakpointvalues (Table 2).

TABLE 12 Minimum inhibitory concentrations (MIC) of B. subtilis 281.Antibiotic resistance test Minimum inhibitory concentration (mg/L) ofantibiotics Strain Ery Gen Tet Str Van Chl Kan Cli B. subtilis 281≤0.125 ≤2 ≤0.125 8 0.25 ≤4 ≤4 2 EFSA breakpoint 4 4 8 8 4 8 8 4 Ery:Erythromycin; Gen: Gentamicin; Tet: Tetracycline; Str: Streptomycin; Vm:Vancomycin; Chl: Chloramphenicol; Kan: Kanamycin; Cli: Clindamycin.

Example 3C Respiratory Tract Infection Test

The survival rate after respiratory tract infection of B. subtilis 281was 100% while the positive control of pathogenic bacteria infectedgroups including S. pneumoniae and B. cereus showed 100% mortality after24 hours (FIG. 9). Lung pictures were taken and showed strong damage inpathogen infected positive groups while lung of B. subtilis 281 infectedgroups showed similar lung status as negative control group (FIG. 10)and any colony of Bacillus was found from the homogenized lung of B.subtilis 281 infected group (data not shown).

Example 3D Efficacy Tests

The antagonism test results of B. subtilis 281 showed inhibited growthof E. coli ATCC 22922, P. aeruginosa, B. cereus ATCC 27348 and S.Typhimurium ATCC 14028 at different degrees (FIG. 11 and Table 13).

TABLE 13 Antagonistic activity of Bacillus subtilis 281 againstpathogens. Pathogens B. subtilis 281 Escherichia coli ATCC 25922 2Pseudomonas aeruginosa ATCC 27853 1 Bacillus cereus ATCC 27348 1Staphylococcus aureus ATCC 6538 NA Salmonella Typhimurium ATCC 14028 2Listeria innocua ATCC 33090 NA NA: No antagonism was observed

B. subtilis 281 antagonism tests against mold showed positive antagonismagainst Alternaria alternata (Fries) Keissler (ATCC® MYA-4642™) andCladosporium sphaerospermum Penzig (ATCC® MYA-4645™) at variable levels(Table 4). The inhibition of the mold growth is evidently expressed as aclear zone around the wells inoculated with the B. subtilis 281 (FIG.12). Penicillium chrysogenum Thom (ATCC® MYA-4644™) was not inhibited atall for any of the strains used on this experiment, however the myceliumcolor around the well inoculated with B. subtilis 281 showed andslightly decrease in the intensity (data not shown) from green to white.

TABLE 14 Antifungal activity of Bacillus subtilis 281 against molds.Inhibition zone (mm) Alternaria alternata Cladosporium Penicillium(Fries) sphaerospermum chrysogenum Keissler Penzig Thom (ATCC (ATCC(ATCC Strain MYA-4642) MYA-4645) MYA-4644) Bacillus 5  5 NA subtilis 281Hydrogen 8 12 10 peroxide 10% NA: No antagonism was observed

Example 3E Taxonomic Identification

The identity of the strain was confirmed as B. subtilis according to theNational Center for Biotechnology Information (NCBI) database. APIresults were monitored for further identification of physiologicalcharacteristics.

Example 3F Complete Genome Sequence

Single run of PacBio provided total number of 99,139 reads whichcomprises in total of 917,648,089 bases. Raw data was assembled usingCanu v1.6 and single contig was produced in size of 4,089,095 base pairs(Separately attached text file of “Bacillus subtilis 281.fasta”). Totalnumber of genes were 4,365 (4,248 coding sequences) and 3,399 annotatedgenes were found which calculated as 80.01% of total genes (Table 5).

Lengthy table referenced here US20200405781A1-20201231-T00003 Pleaserefer to the end of the specification for access instructions.

Example 4 Materials and Methods

As described above.

Example 4A In-Vitro Safety Evaluation of Lecithinase and HemolysisActivity

B. subtilis 3, B. subtilis 281 and B. amyloliquefaciens 298 did not showlecithinase activity observed as the absence of withe precipitatedaround the Bacillus colonies and all strains showed negative reactionfor hemolysis as well.

TABLE 16 Lecithinase and hemolysis activity of B. subtilis strain 3, B.subtilis 281 and B. amyloliquefaciens 298 and B. cereus ATCC 27348.Lecithinase Hemolysis Strain activity activity Bacillus subtilis 3Negative Gamma Bacillus subtilis 281 Negative Gamma Bacillusamyloliquefaciens 298 Negative Gamma Bacillus cereus ATCC 27348 PositiveBeta (positive control)

Example 4B In-Vitro Evaluation of Antibiotic Resistance

An agar dilution was used to evaluate the minimal inhibitoryconcentration (MIC) of antibiotics. B. subtilis 3, B. subtilis 281 andB. amyloliquefaciens 298 were found to be sensitive to erythromycin,gentamicin, tetracycline, streptomycin, vancomycin, chloramphenicol,kanamycin and clindamycin according to the European Food SafetyAuthority MIC breakpoints for Bacillus species. The determined MICvalues are clearly below or equal to the EFSA breakpoint values (Table17).

TABLE 17 Minimum inhibitory concentrations (MIC) of B. subtilis strainsnumber 3, B. subtilis strain 3, B. subtilis 281 and B. amyloliquefaciens298. Antibiotic resistance test Minimum inhibitory concentration (mg/L)of antibiotics Strain Ery Gen Tet Str Van Chl Kan Cli B. subtilis 3 ≤2≤2 ≤4 8 ≤2 ≤4 ≤4 4 B. subtilis 281 ≤0.125 ≤2 ≤0.125 8 0.25 ≤4 ≤4 2 B.amyloliquefaciens 298 ≤0.125 ≤2 ≤0.125 8 0.25 ≤4 ≤4 0.5 EFSA breakpoint4 4 8 8 4 8 8 4 Ery: Erythromycin; Gen: Gentamicin; Tet: Tetracycline;Str: Streptomycin; Vm: Vancomycin; Chl: Chloramphenicol; Kan: Kanamycin;Cli: Clindamycin.

Example 4C Respiratory Tract Infection Test

The survival rate after respiratory tract infection of B. subtilis 3, B.subtilis 281 and B. amyloliquefaiciens 298 was 100% while the positivecontrol of pathogenic bacteria infected groups including S. pneumoniaeand B. cereus showed 100% mortality after 24 hours (FIG. 17). All lungpictures were taken and showed strong damage in pathogen infectedpositive groups while lung of B. subtilis 3, B. subtilis 281 and B.amyloliquefaiciens 298 infected groups showed similar lung status asnegative control group (FIG. 18) and any colony forming units ofBacillus strains were found from the homogenized lung of B. subtilis 3,B. subtilis 281 and B. amyloliquefaiciens 298 infected groups (data notshown).

Example 4D Efficacy Tests

The antagonism test results of B. subtilis 3, B. subtilis 281 and B.amyloliquefaiciens 298 against pathogenic bacteria indicate that B.subtilis 3 reduce the growth of E. coli ATCC 22922, S. aureus ATCC 11335and L. inocua ATCC 3586 at various levels. Regarding to B. subtilis 281and B. amyloliquefaiciens 298, they seem to antagonize the growing of E.coli ATCC 22922, P. aeruginosa, B. cereus ATCC 27348 and S. typhi ATCC14028 also at different degrees. In addition, B. amyloliquefaiciens 298has also the ability of slightly reduce the growth of S. aureus ATCC11335. In general, B. amyloliquefaiciens 298 could be more effectiveagainst pathogenic bacteria than the other two strains (FIG. 19).

TABLE 18 Antagonistic activity of Bacillus subtilis strains againstpathogens. Pathogens Inhibition zone (mm) B. B. B. Bacillus strainssubtilis 3 subtilis 281 amyloliquefaiciens 298 Escherichia coli 1 2 2ATCC 22922 Pseudomonas NA 1 1 aeruginosa Bacillus cereus NA 1 2 ATCC27348 Staphylococcus 1 NA 1 aureus ATCC 11335 Salmonella typhi NA 2 2ATCC 14028 Listeria inocua 2 NA NA ATCC 3586 NA: No antagonism wasobserved

B. subtilis 3, B. subtilis 281 and B. amyloliquefaiciens 298 antagonismagainst mold indicate the strain 3, 281 and 298 has antagonism againstAlternaria alternata (Fries) Keissler (ATCC® MYA-4642™) and Cladosporiumsphaerospermum Penzig (ATCC® MYA-4645™) at variable level (Table 19).The inhibition of the mold growth is evidently expressed as a clear zonearound the wells inoculated with the B. subtilis 3, B. subtilis 281 andB. amyloliquefaiciens 298 (FIG. 20). Penicillium chrysogenum Thom (ATCC®MYA-4644™) was not inhibited at all for any of the strains used on thisexperiment, however the mycelium color around the well inoculated withstrains number 281 and 298 show and slightly decrease in the intensity(data not shown) from green to white.

TABLE 19 Antifungal activity of Bacillus subtilis strains against molds.Inhibition zone (mm) Alternaria alternata Cladosporium Penicillium(Fries) sphaerospermum chrysogenum Keissler Penzig Thom (ATCC (ATCC(ATCC Strain MYA-4642) MYA-4645) MYA-4644) Bacillus 2 4 NA subtilis 3Bacillus 5 5 NA subtilis 281 Bacillus 6 6 NA amyloliquefaciens 298Hydrogen 8 12  10 peroxide 10% NA: No antagonism was observed

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims.

All publications, patents and patent applications mentioned in thisspecification are herein incorporated in their entirety by referenceinto the specification, to the same extent as if each individualpublication, patent or patent application was specifically andindividually indicated to be incorporated herein by reference. Inaddition, citation or identification of any reference in thisapplication shall not be construed as an admission that such referenceis available as prior art to the present invention. To the extent thatsection headings are used, they should not be construed as necessarilylimiting. In addition, any priority document(s) of this applicationis/are hereby incorporated herein by reference in its/their entirety.

REFERENCES

-   1. Cho, K.-M. (2008). “Characterization of potential probiotics    Bacillus subtilis CS90 from soybean paste (doenjang) and its    antimicrobial activity against food-borne pathogens.” Journal of    Applied Biological Chemistry 51(6): 285-291.-   2. FRANZ, C. M., A. HUMMEL and W. H. HOLZAPFEL (2005). “Problems    related to the safety assessment of lactic acid bacteria starter    cultures and probiotics.” Mitteilungen aus Lebensmitteluntersuchung    and Hygiene 96(1): 39-65.-   3. Ginsberg, H. S., L. L. Moldawer, P. B. Sehgal, M.    Redington, P. L. Kilian, R. M. Chanock and G. A. Prince (1991). “A    mouse model for investigating the molecular pathogenesis of    adenovirus pneumonia.” Proceedings of the National Academy of    Sciences 88(5): 1651-1655.-   4. Holzapfel, W. H. and U. Schillinger (2002). “Introduction to    pre-and probiotics.” Food Research International 35(2): 109-116.-   5. Hong, H., J. M. Huang, R. Khaneja, L. Hiep, M. Urdaci and S.    Cutting (2008). “The safety of Bacillus subtilis and Bacillus    indicus as food probiotics.” Journal of applied microbiology 105(2):    510-520.-   6. Jeon, H. H., J. Y. Jung, B.-H. Chun, M.-D. Kim, S. Y. Baek, J. Y.    Moon, S.-H. Yeo and C. O. Jeon (2016). “Screening and    characterization of potential Bacillus starter cultures for    fermenting low salt soybean paste (doenjang).” J. Microbiol.    Biotechnol 26(4): 666-674.-   7. Jorgensen, J. H. and J. D. Turnidge (2015). Susceptibility test    methods: dilution and disk diffusion methods. Manual of Clinical    Microbiology, Eleventh Edition, American Society of Microbiology:    1253-1273.-   8. Kong, X., G. R. Hellermann, G. Patton, M. Kumar, A. Behera, T. S.    Randall, J. Zhang, R. F. Lockey and S. S. Mohapatra (2005). “An    immunocompromised BALB/c mouse model for respiratory syncytial virus    infection.” Virology journal 2(1): 3.-   9. Leuschner, R. G., T. P. Robinson, M. Hugas, P. S. Cocconcelli, F.    Richard-Forget, G. Klein, T. R. Licht, C. Nguyen-The, A. Querol    and M. Richardson (2010). “Qualified presumption of safety (QPS): a    generic risk assessment approach for biological agents notified to    the European Food Safety Authority (EFSA).” Trends in Food Science &    Technology 21(9): 425-435.-   10. Reysenbach, A.-L., L. J. Giver, G. S. Wickham and N. R. Pace    (1992). “Differential amplification of rRNA genes by polymerase    chain reaction.” Applied and Environmental Microbiology 58(10):    3417-3418.-   11. Sorokulova, I. B., I. V. Pinchuk, M. Denayrolles, I. G.    Osipova, J. M. Huang, S. M. Cutting and M. C. Urdaci (2008). “The    safety of two Bacillus probiotic strains for human use.” Digestive    diseases and sciences 53(4): 954-963.-   12. Wang, L.-T., F.-L. Lee, C.-J. Tai and H. Kasai (2007).    “Comparison of gyrB gene sequences, 16S rRNA gene sequences and    DNA-DNA hybridization in the Bacillus subtilis group.” International    Journal of Systematic and Evolutionary Microbiology 57(8):    1846-1850.-   13. Xu, S. J., D. H. Park, J.-Y. Kim and B.-S. Kim (2016).    “Biological control of gray mold and growth promotion of tomato    using Bacillus spp. isolated from soil.” Tropical Plant Pathology    41(3): 169-176.

LENGTHY TABLES The patent application contains a lengthy table section.A copy of the table is available in electronic form from the USPTO website(https://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20200405781A1).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

What is claimed is:
 1. A composition comprising at least two bacterialstrains selected from the group consisting of Bacillus subtilis 281,Bacillus subtilis 3, Bacillus amyloliquefaciens 298 and a functionalhomolog of any of the preceding, wherein the composition does notcomprise more than 5 different species of microbes, wherein: a sample ofBacillus subtilis 281, has been deposited as KCTC 13468BP at the KoreanCollection for Type Cultures; a sample of Bacillus subtilis 3, has beendeposited as KCTC 13467BP at the Korean Collection for Type Cultures;and a sample of Bacillus amyloliquefaciens 298, has been deposited asKCTC 13469BP at the Korean Collection for Type Cultures.
 2. An articleof manufacture comprising at least two bacterial strains selected fromthe group consisting of Bacillus subtilis 281, Bacillus subtilis 3,Bacillus amyloliquefaciens 298 and a functional homolog of any of thepreceding, wherein the composition does not comprise more than 5different species of microbes, wherein: a sample of Bacillus subtilis281, has been deposited as KCTC 13468BP at the Korean Collection forType Cultures; a sample of Bacillus subtilis 3, has been deposited asKCTC 13467BP at the Korean Collection for Type Cultures; and a sample ofBacillus amyloliquefaciens 298, has been deposited as KCTC 13469BP atthe Korean Collection for Type Cultures.
 3. The composition of claim 1,wherein said bacterial strain or functional homolog of same is attachedto a solid support.
 4. The composition of claim 1, wherein saidbacterial strain or functional homolog of same is soluble.
 5. Thearticle of manufacture of claim 2 comprising a commodity selected fromthe group consisting of a food, a feed, a beverage, a pharmaceutical, anutraceutical, a cosmetic, a filter, a matrix and an aerosol system. 6.An aerosol dispensing device comprising an effective amount of at leasttwo bacterial strains selected from the group consisting of Bacillussubtilis 281, Bacillus subtilis 3, Bacillus amyloliquefaciens 298 and afunctional homolog of any of the preceding, wherein the composition doesnot comprise more than 5 different species of microbes, wherein: asample of Bacillus subtilis 281, has been deposited as KCTC 13468BP atthe Korean Collection for Type Cultures; a sample of Bacillus subtilis3, has been deposited as KCTC 13467BP at the Korean Collection for TypeCultures; and a sample of Bacillus amyloliquefaciens 298, has beendeposited as KCTC 13469BP at the Korean Collection for Type Cultures. 7.The aerosol dispensing device of claim 6 being automated.
 8. Thecomposition of claim 1, wherein said bacterial strain or said functionalhomolog comprises a genomic nucleic acid sequence at least 97% identicalto the nucleic acid sequence set forth in SEQ ID NO: 4, 6 or
 8. 9. Thecomposition of claim 1, wherein said bacterial strain or said functionalhomolog exhibits: (i) growth inhibitory effects against bacteria andfungi, as shown in Tables 3, 4, 8, 9, 13, 14, 18 and
 19. (ii) nolecithinase activity as determined by the absence of a white precipitatewhen the isolated bacterial strain or functional homolog of same isstreaked out onto egg yolk agar and incubated for 24 h at 37° C.; and(iii) gamma hemolytic activity when streaked onto 5% sheep blood agarand incubated for 24 h at 37° C.
 10. The composition of claim 1, whereinthe bacterial strain or functional homolog of same is sensitive to anantibiotic selected from the group consisting of erythromycin,gentamicin, tetracycline, streptomycin, vancomycin, chloramphenicol,kanamycin and clindamycin according to the European Food SafetyAuthority MIC breakpoints for Bacillus species.
 11. The composition ofclaim 1, wherein the bacterial strain or functional homolog of same isincapable of colonizing a mammalian lung.
 12. The composition of claim1, wherein the bacterial strain or functional homolog of same exhibitsgrowth inhibitory effects against bacteria and fungi, as shown in Tables3, 4, 8, 9, 13, 14, 18 and
 19. 13. The composition of claim 1, whereinsaid functional homolog is characterized by at least one of: at least70% DNA-DNA relatedness to the deposited strain with 5 uC or less DTm;at least 97% genomic DNA sequence identity to the genomic DNA sequenceof the deposited strain; having an average nucleotide identity (ANI) ofat least about 97% with the deposited strain; having a tetranucleotidesignature frequency correlation coefficient of at least about 0.99 withthe deposited strain; having a Dice similarity coefficient; being of thesame ribotype as that of the deposited strain; having a Pearsoncorrelation coefficient of at least about 0.99 with the depositedstrain; having a multilocus sequence typing (MLST) of at least about0.99 with the deposited strain; having a functionality conserved genethat is at least about 97% identical to that of the deposited strain asdetermined at a level of a single gene or multilocus sequence analysis(MLSA); having a 16S nucleic acid sequence that is at least about 97%identical to that of the deposited strain; having substantially the samebiochemical profiling as determined by the GEN III redox chemistry;maintaining the coding and/or non-coding sequence order as that of thedeposited strain; having the same codon usage as that of the depositedstrain.
 14. The composition of claim 1, comprising Bacillus subtilis281, Bacillus subtilis 3 and Bacillus amyloliquefaciens 298 or afunctional homolog of same.
 15. The composition of claim 14, whereinsaid Bacillus subtilis 281, Bacillus subtilis 3 and Bacillusamyloliquefaciens 298 or a functional homolog of same are present in aratio of about 1:1:1.
 16. A method of controlling a population ofpathogenic bacteria and/or fungi, the method comprising providing aneffective amount of the composition of claim 1, thereby controlling thepopulation of pathogenic bacteria and/or fungi.
 17. The method of claim16, wherein said providing is by inhalation or oral administration. 18.The method of claim 16, wherein said contacting comprises in vitrocontacting.
 19. The method of claim 16, wherein said providing is byusing an aerosol dispensing device.